roboneuro 0.1.1

data/spec/processor_spec.rb

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+require_relative 'spec_helper'
+require 'nokogiri'
+
+describe Whedon::Processor do
+  subject(:paper) { Whedon::Paper.new(17, nil, 'fixtures/paper/paper.md') }
+  subject(:paper_with_funky_bib_path) { Whedon::Paper.new(17, nil, 'fixtures/paper/paper-bib.md') }
+
+  subject(:processor) { Whedon::Processor.new(17, File.read('fixtures/review_body.txt')) }
+
+  context "Without CURRENT_ISSUE and CURRENT_VOLUME in ENV" do
+    before do
+      ENV["JOURNAL_LAUNCH_DATE"] = Time.now.strftime('%F')
+      processor.paper = paper
+    end
+
+    after do
+      FileUtils.rm_rf("fixtures/paper/10.21105.joss.00017.crossref.xml")
+    end
+
+    it "should know how to initialize properly" do
+      expect(processor.review_issue_id).to eql(17)
+      expect(processor.current_volume).to eql(1)
+      expect(processor.current_issue).to eql(1)
+    end
+
+    it "should know how to find papers to be compiled" do
+      expect(processor.find_paper_paths('fixtures/test_paper').size).to eql(2)
+      expect(processor.find_paper_paths('fixtures/test_paper')).to include("fixtures/test_paper/paper.md")
+    end
+
+    it "should know how to find latex papers to be compiled" do
+      expect(processor.find_paper_paths('fixtures/latex_paper').size).to eql(1)
+      expect(processor.find_paper_paths('fixtures/latex_paper')).to include("fixtures/latex_paper/paper.tex")
+    end
+
+    it "should know how to compile Crossref XML" do
+      VCR.use_cassette('joss-lookup') do
+        ENV['JOURNAL_URL'] = 'http://joss.theoj.org'
+        expect(paper_with_funky_bib_path.bibtex_path).to eq("fixtures/paper/weird-bib-path.bib")
+        generated = processor.generate_crossref
+        expect(generated).to eql("fixtures/paper/10.21105.joss.00017.crossref.xml")
+      end
+    end
+  end
+
+  context "with CURRENT_ISSUE and CURRENT_VOLUME overridden" do
+    before do
+      ENV["JOURNAL_LAUNCH_DATE"] = Time.now.strftime('%F')
+      ENV["CURRENT_ISSUE"] = "12344"
+      ENV["CURRENT_VOLUME"] = "12"
+      processor.paper = paper
+    end
+
+    after do
+      FileUtils.rm_rf("fixtures/paper/10.21105.joss.00017.crossref.xml")
+      ENV["CURRENT_ISSUE"] = nil
+      ENV["CURRENT_VOLUME"] = nil
+    end
+
+    it "should know how to initialize properly" do
+      expect(processor.review_issue_id).to eql(17)
+      expect(processor.current_volume).to eql("12")
+      expect(processor.current_issue).to eql("12344")
+    end
+  end
+end

data/spec/review_spec.rb

@@ -0,0 +1,12 @@
+require_relative 'spec_helper'
+
+describe Whedon::Review do
+
+  subject { Whedon::Review.new(17, ENV['REVIEW_REPOSITORY']) }
+
+  it "can should return the correct number of review issues" do
+    VCR.use_cassette('review') do
+      expect(subject.issue_body).to match(/Submitting author/)
+    end
+  end
+end

data/spec/reviews_spec.rb

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+require_relative 'spec_helper'
+
+describe Whedon::Reviews do
+
+  subject { Whedon::Reviews.new(ENV['REVIEW_REPOSITORY']) }
+
+  it "can return #review issues" do
+    VCR.use_cassette('reviews') do
+      expect(subject.list_current.first[1]).to have_key(:opened_at)
+    end
+  end
+
+  it "can should return the correct number of review issues" do
+    VCR.use_cassette('reviews') do
+      expect(subject.list_current.size).to eql(5)
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,22 @@
+require "bundler/setup"
+require "fileutils"
+require "vcr"
+
+VCR.configure do |config|
+  config.cassette_library_dir = "fixtures/vcr_cassettes"
+  config.hook_into :webmock
+  config.filter_sensitive_data("<GITHUB_TOKEN>") { ENV['GH_TOKEN'] }
+end
+
+require_relative "../lib/whedon"
+
+# FIXME: This is kind of gross.
+# Rugged needs there to be a Git repo present in the fixtures folder when
+# running tests (spec/whedon_spec.rb#L11). Also, we're hard-coding the path
+# to tmp/#{review_issue_id} so we need a fixture there.
+Dir.mkdir('tmp') unless Dir.exist?('tmp')
+FileUtils.rm_r('tmp/17') if Dir.exist?('tmp/17')
+FileUtils.copy_entry('fixtures/paper', 'tmp/17')
+
+# Any git repo will do (using the one from Whedon)
+FileUtils.copy_entry('.git', 'tmp/17/.git')

data/spec/whedon_spec.rb

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+require_relative 'spec_helper'
+
+describe Whedon do
+
+  subject(:paper) { Whedon::Paper.new(17, nil, 'fixtures/paper/paper.md') }
+  subject(:paper_with_one_author) { Whedon::Paper.new(17, nil, 'fixtures/paper/paper-single-author.md') }
+  subject(:paper_with_harder_names) { Whedon::Paper.new(17, nil, 'fixtures/paper/paper-with-harder-names.md') }
+
+  it "should initialize properly" do
+    expect(paper.review_issue_id).to eql(17)
+    expect(paper.authors.size).to eql(2)
+    expect(paper.authors.first.affiliation).to eql('GitHub Inc., Disney Inc.')
+    expect(paper.paper_path).to eql('fixtures/paper/paper.md')
+    expect(paper.bibliography_path).to eql('paper.bib')
+  end
+
+  it "should know what the review_issue_url is" do
+    expect(paper.review_issue_url).to eql("https://github.com/#{ENV['REVIEW_REPOSITORY']}/issues/17")
+  end
+
+  it "should know how to generate joss_id" do
+    expect(paper.joss_id).to eql("joss.00017")
+  end
+
+  it "should know how to generate the formatted_doi" do
+    expect(paper.formatted_doi).to eql("10.21105/joss.00017")
+  end
+
+  it "should know how to generate the filename_doi" do
+    expect(paper.filename_doi).to eql("10.21105.joss.00017")
+  end
+
+  it "should know how to generate the joss_resource_url" do
+    expect(paper.joss_resource_url).to eql("#{ENV['JOURNAL_URL']}/papers/10.21105/joss.00017")
+  end
+
+  it "should know how to generate the paper#pdf_url" do
+    expect(paper.pdf_url).to eql("http://www.theoj.org/joss-papers-testing/joss.00017/10.21105.joss.00017.pdf")
+  end
+
+  it "should know what the paper#paper_org is" do
+    expect(paper.paper_org).to eql("openjournals")
+  end
+
+  it "should know what the paper#paper_repo is" do
+    expect(paper.paper_repo).to eql("joss-papers-testing")
+  end
+
+  it "should know what its tags are" do
+    expect(paper.tags).to eql(["example", "tags", "for the paper"])
+  end
+
+  it "should know how generate_authors" do
+    authors_xml = Nokogiri::XML(paper.crossref_authors)
+    expect(authors_xml.search('person_name').size).to eql(2)
+    expect(authors_xml.search('person_name[sequence="first"]').size).to eql(1)
+    expect(authors_xml.search('person_name[sequence="additional"]').size).to eql(1)
+    expect(authors_xml.xpath('//ORCID').first.text).to eql("http://orcid.org/0000-0002-3957-2474")
+  end
+
+  it "should know how to format citation strings for multi-author papers" do
+    expect(paper.authors.size).to eql(2)
+    expect(paper.authors.first.name).to eql('Arfon Smith')
+    expect(paper.citation_author).to eql("Smith et al.")
+  end
+
+  it "should know how to format citation strings for single-author papers" do
+    expect(paper_with_one_author.authors.size).to eql(1)
+    expect(paper_with_one_author.citation_author).to eql("Smith, A. M.")
+  end
+
+  it "should know how to format citation strings for multi-author papers" do
+    expect(paper_with_harder_names.authors.size).to eql(2)
+    expect(paper_with_harder_names.citation_author).to eql("Smith et al.")
+    expect(paper_with_harder_names.authors.last.last_name).to eq('van Dishoeck')
+  end
+
+  it "should fail to initialize when authors don't have affiliations" do
+    expect { Whedon::Paper.new(17, nil, 'fixtures/paper/paper-with-missing-affiliations.md') }.to raise_error("Author (Arfon M Smith) is missing affiliation")
+  end
+
+  it "should fail to initialize when title is missing" do
+    expect { Whedon::Paper.new(17, nil, 'fixtures/paper/paper_with_missing_title.md') }.to raise_error(/Paper YAML header is missing expected fields: title/)
+  end
+
+  it "should know how to generate the deposit_payload" do
+    VCR.use_cassette('review') do
+      %w{title tags languages authors doi archive_doi repository_address editor reviewers}.each do |attribute|
+        expect(paper_with_harder_names.deposit_payload['paper'][attribute].nil?).to be_falsey
+      end
+    end
+  end
+end

metadata

@@ -0,0 +1,386 @@
+--- !ruby/object:Gem::Specification
+name: roboneuro
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+platform: ruby
+authors:
+- Agah Karakuzu
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2022-04-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bibtex-ruby
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 6.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 6.0.0
+- !ruby/object:Gem::Dependency
+  name: dotenv
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: latex-decode
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: github-linguist
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.3'
+- !ruby/object:Gem::Dependency
+  name: openjournals-nameable
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: octokit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.20'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.20'
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '1.8'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '1.8'
+- !ruby/object:Gem::Dependency
+  name: redcarpet
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+- !ruby/object:Gem::Dependency
+  name: tilt
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.19'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.19'
+- !ruby/object:Gem::Dependency
+  name: unicode
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.4.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.4.4
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.10'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+- !ruby/object:Gem::Dependency
+  name: vcr
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '6.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '6.0'
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.11.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.11.2
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.10.8
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.10.8
+description:
+email:
+- agahkarakuzu@gmail.com
+executables:
+- whedon
+extensions: []
+extra_rdoc_files: []
+files:
+- ".DS_Store"
+- ".env-example"
+- ".env.test"
+- ".github/workflows/docker-image.yml"
+- ".github/workflows/tests.yml"
+- ".gitignore"
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.md
+- Rakefile
+- bin/whedon
+- fixtures/latex_paper/paper.tex
+- fixtures/paper/10.21105.jcon.00017.crossref.xml
+- fixtures/paper/crossref-metadata.yaml
+- fixtures/paper/paper-bib.md
+- fixtures/paper/paper-single-author.md
+- fixtures/paper/paper-with-harder-names.md
+- fixtures/paper/paper-with-missing-affiliations.md
+- fixtures/paper/paper.bib
+- fixtures/paper/paper.html
+- fixtures/paper/paper.md
+- fixtures/paper/paper.pdf
+- fixtures/paper/paper.xml
+- fixtures/paper/paper_with_missing_title.md
+- fixtures/review_body.txt
+- fixtures/test_paper/nested/paper.bib
+- fixtures/test_paper/nested/paper.md
+- fixtures/test_paper/paper.bib
+- fixtures/test_paper/paper.md
+- fixtures/vcr_cassettes/joss-lookup.yml
+- fixtures/vcr_cassettes/review.yml
+- fixtures/vcr_cassettes/reviews.yml
+- lib/whedon.rb
+- lib/whedon/auditor.rb
+- lib/whedon/author.rb
+- lib/whedon/bibtex_parser.rb
+- lib/whedon/compilers.rb
+- lib/whedon/github.rb
+- lib/whedon/orcid_validator.rb
+- lib/whedon/processor.rb
+- lib/whedon/review.rb
+- lib/whedon/reviews.rb
+- lib/whedon/version.rb
+- paperdraft.Dockerfile
+- pkg/roboneuro-0.1.0.gem
+- resources/.DS_Store
+- resources/NeuroLibre/.DS_Store
+- resources/NeuroLibre/aas-logo.png
+- resources/NeuroLibre/apa.csl
+- resources/NeuroLibre/defaults.yaml
+- resources/NeuroLibre/latex.template
+- resources/NeuroLibre/logo.png
+- resources/NeuroLibre/logo_link.png
+- resources/apa.csl
+- resources/crossref.template
+- resources/docker-defaults.yaml
+- resources/docker-entrypoint.sh
+- resources/jats.csl
+- resources/jats.template
+- resources/jose/apa.csl
+- resources/jose/defaults.yaml
+- resources/jose/latex.template
+- resources/jose/logo.png
+- resources/joss/aas-logo.png
+- resources/joss/apa.csl
+- resources/joss/defaults.yaml
+- resources/joss/latex.template
+- resources/joss/logo.png
+- resources/latex.template
+- resources/time.lua
+- roboneuro.gemspec
+- spec/auditor_spec.rb
+- spec/author_spec.rb
+- spec/bibtex_spec.rb
+- spec/orcid_validator_spec.rb
+- spec/processor_spec.rb
+- spec/review_spec.rb
+- spec/reviews_spec.rb
+- spec/spec_helper.rb
+- spec/whedon_spec.rb
+homepage: https://github.com/neurolibre/roboneuro-gem
+licenses:
+- MIT
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.0.9
+signing_key:
+specification_version: 4
+summary: A collection of command-line utilities to manage NeuroLibre submissions.
+test_files:
+- spec/auditor_spec.rb
+- spec/author_spec.rb
+- spec/bibtex_spec.rb
+- spec/orcid_validator_spec.rb
+- spec/processor_spec.rb
+- spec/review_spec.rb
+- spec/reviews_spec.rb
+- spec/spec_helper.rb
+- spec/whedon_spec.rb