neurolibre 1.5.3

checksums.yaml

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+---
+SHA256:
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+  data.tar.gz: 011d818ffd6862603ab817e359cedcd344c1c6263703cac5004f1ca8339a8003
+SHA512:
+  metadata.gz: ff5f5745c38a93662bca47cf623671c34b4784217270762a66a3b489082feadc072f94996c954b1d20bd8e52571355feeade515811315cdaccd75e77c2157cb4
+  data.tar.gz: 777020c7718448df0b583fc5dc82e7cc3df8ad3b5e699853328a92bd4c946dd7f998b0dc20db903f82346d587c243b546ee02a38bf33453de9632024085b2a08

data/CHANGELOG.md

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+# Changelog
+
+## 1.5.2 (2022-10-29)
+
+- Updated journal data for JuliaCon
+
+## 1.5.1 (2022-10-25)
+
+- Remove newlines from paper's title
+- Faraday and Octokit dependencies updated to latest major versions
+
+## 1.5.0 (2022-10-02)
+
+- Added Commonmarker as dependency
+- Submission metadata's title is converted to plain text
+
+## 1.4.1 (2022-09-28)
+
+- Added method to Submission to get track information
+
+## 1.4.0 (2022-08-01)
+
+- Added method to Journal to get year/volume/issue information for any date
+- Submission metadata now takes into account published paper status
+
+## 1.3.6 (2022-07-11)
+
+- Improve parsing of author names
+
+## 1.3.5 (2022-07-01)
+
+- Added configuration for JuliaCon
+
+## 1.3.4 (2022-05-29)
+
+- Use Faraday v2 (updated Octokit and other dependencies)
+
+## 1.3.3 (2022-03-31)
+
+- Fix bug with upcased user logins
+
+## 1.3.2 (2022-03-17)
+
+- Allow setting GitHub access using GITHUB_TOKEN env var
+
+## 1.3.1 (2022-03-09)
+
+- Fix error when loading metadata for papers with wrong path
+
+## 1.3.0 (2022-03-02)
+
+- Change branches using git-switch instead of git-checkout to remove ambiguaties. Requires Git >= 2.23
+
+## 1.2.1 (2021-11-30)
+
+- Changed metadata dates format to ISO
+- Changed editor and reviewers metadata values to github login
+- Removed languages from article metadata
+
+## 1.2.0 (2021-11-23)
+
+- Added reviews_repository_url to Journal
+- Added article_metadata to Submission
+- Added editor and paper dates lookup information in Submission
+- Fixed error reading reviewers list from issue body
+
+## 1.1.1 (2021-11-05)
+
+- Added support for test-journal
+
+## 1.1.0 (2021-10-29)
+
+- Added Theoj::PublishedPaper object with metadata from Journal's API
+- Added custom Error class
+
+## 1.0.0 (2021-10-20)
+
+- Added method to Journal to create paper_id from issue_id
+- Added method to Journal to get a DOI based on a paper id
+- Added languages to Paper
+- Added authors info to Paper
+- Author object
+- Added ORCID validation
+- Added Submission object, grouping a paper, a review issue and a journal
+- Added paper depositing
+
+## 0.0.3 (2021-10-08)
+
+- Added metadata methods to Paper
+- Added to ReviewIssue: editor, reviewers, archive, version
+- New method to read any value from review's issue body
+- Values read from issue boy will be empty if Pending or TBD
+- Added journal config data for OpenJournals: JOSS and JOSE
+
+
+## 0.0.2 (2021-09-22)
+
+- Available objects: Theoj::Journal, Theoj::ReviewIssue and Theoj::Paper
+
+
+## 0.0.1 (2021-09-22)
+
+- Gem created
+

data/LICENSE

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+MIT License
+
+Copyright (c) 2021 Juanjo Bazán
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

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+# The Open Journal
+A library to manage editorial objects used by the open journals review process
+
+[![CI](https://github.com/xuanxu/theoj/actions/workflows/ci.yml/badge.svg)](https://github.com/xuanxu/theoj/actions/workflows/ci.yml)
+[![Gem Version](https://badge.fury.io/rb/theoj.svg)](https://badge.fury.io/rb/theoj)

data/lib/neurolibre.rb

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+require_relative "theoj/version"
+require_relative "theoj/git"
+require_relative "theoj/github"
+require_relative "theoj/orcid"
+require_relative "theoj/published_paper"
+require_relative "theoj/submission"
+require_relative "theoj/journal"
+require_relative "theoj/review_issue"
+require_relative "theoj/paper"
+require_relative "theoj/author"
+
+module Theoj
+  class Error < StandardError; end
+end

data/lib/theoj/author.rb

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+require "nameable"
+
+module Theoj
+  class Author
+    attr_accessor :name
+    attr_accessor :orcid
+    attr_accessor :affiliation
+
+    AUTHOR_FOOTNOTE_REGEX = /^[^\^]*/
+
+    # Initialized with authors & affiliations block in the YAML header from an Open Journal paper
+    # e.g. https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography
+    def initialize(name, orcid, index, affiliations_hash)
+      parse_name name
+      @orcid = validate_orcid orcid
+      @affiliation = build_affiliation_string(index, affiliations_hash)
+    end
+
+    def given_name
+      @parsed_name.first
+    end
+
+    def middle_name
+      @parsed_name.middle
+    end
+
+    def last_name
+      @parsed_name.last
+    end
+
+    def initials
+      [@parsed_name.first, @parsed_name.middle].compact.map {|v| v[0] + "."} * ' '
+    end
+
+    def to_h
+      {
+        given_name: given_name,
+        middle_name: middle_name,
+        last_name: last_name,
+        orcid: orcid,
+        affiliation: affiliation
+      }
+    end
+
+    private
+
+    def parse_name(author_name)
+      if author_name.is_a? Hash
+        g = author_name["given-names"] || author_name["given"] || author_name["first"] || author_name["firstname"]
+        m = author_name["dropping-particle"]
+        s = author_name["surname"] || author_name["family"]
+
+        g = strip_footnotes(g) unless g.nil?
+        s = strip_footnotes(s) unless s.nil?
+
+        @parsed_name = m.nil? ? Nameable::Latin.new(g, s) : Nameable::Latin.new(g, m, s)
+      else
+        @parsed_name = Nameable::Latin.new.parse(strip_footnotes(author_name))
+      end
+
+      @name = @parsed_name.to_nameable
+    end
+
+    # Input: Arfon Smith^[Corresponding author: arfon@example.com]
+    # Output: Arfon Smith
+    def strip_footnotes(author_name)
+      author_name.to_s[AUTHOR_FOOTNOTE_REGEX]
+    end
+
+    def validate_orcid(author_orcid)
+      return nil if author_orcid.to_s.strip.empty?
+
+      validator = Theoj::Orcid.new(author_orcid)
+      if validator.valid?
+        return author_orcid.strip
+      else
+        raise Theoj::Error, "Problem with ORCID (#{author_orcid}) for #{self.name}. #{validator.error}"
+      end
+    end
+
+    # Takes the author affiliation index and a hash of all affiliations and
+    # associates them. Then builds the author affiliation string
+    def build_affiliation_string(index, affiliations_hash)
+      return nil if index.nil? # Some authors don't have an affiliation
+
+      # If multiple affiliations, parse each one and build the affiliation string
+      author_affiliations = []
+
+      # Turn YAML keys into strings so that mixed integer and string affiliations work
+      affiliations_hash.transform_keys!(&:to_s)
+
+      affiliations = index.to_s.split(',').map(&:strip)
+
+      # Raise if we can't parse the string, might be because of this bug :-(
+      # https://bugs.ruby-lang.org/issues/12451
+      affiliations.each do |a|
+        raise Theoj::Error, "Problem with affiliations for #{self.name}, perhaps the " +
+              "affiliations index need quoting?" unless affiliations_hash.has_key?(a)
+
+        author_affiliations << affiliations_hash[a].strip
+      end
+
+      author_affiliations.join(', ')
+    end
+
+  end
+end

data/lib/theoj/git.rb

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+require "open3"
+require "fileutils"
+
+module Theoj
+  module Git
+    def clone_repo(url, local_path)
+      url = URI.extract(url.to_s).first
+      return false if url.nil?
+
+      FileUtils.mkdir_p(local_path)
+      stdout, stderr, status = Open3.capture3 "git clone #{url} #{local_path}"
+      status.success?
+    end
+
+    def change_branch(branch, local_path)
+      return true if (branch.nil? || branch.strip.empty?)
+      stdout, stderr, status = Open3.capture3 "git -C #{local_path} switch #{branch}"
+      status.success?
+    end
+  end
+end

data/lib/theoj/github.rb

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+require "octokit"
+
+# This module includes all the methods involving calls to the GitHub API
+# It reuses a memoized Octokit::Client instance
+module Theoj
+  module GitHub
+
+    # Authenticated Octokit
+    def github_client
+      @github_client ||= Octokit::Client.new(access_token: github_access_token, auto_paginate: true)
+    end
+
+    # GitHub access token
+    def github_access_token
+      @github_access_token ||= (ENV["GH_ACCESS_TOKEN"] || ENV["GITHUB_TOKEN"])
+    end
+
+    # GitHub API headers
+    def github_headers
+      @github_headers ||= { "Authorization" => "token #{github_access_token}",
+                            "Content-Type" => "application/json",
+                            "Accept" => "application/vnd.github.v3+json" }
+    end
+
+    # Return an Octokit GitHub Issue
+    def issue(repo, issue_id)
+      @issue ||= github_client.issue(repo, issue_id)
+    end
+
+    # List labels of a GitHub issue
+    def issue_labels(repo, issue_id)
+      github_client.labels_for_issue(repo, issue_id).map { |l| l[:name] }
+    end
+
+    # Uses the GitHub API to determine if a user is already a collaborator of the repo
+    def is_collaborator?(repo, username)
+      username = user_login(username)
+      github_client.collaborator?(repo, username)
+    end
+
+    # Uses the GitHub API to determine if a user is already a collaborator of the repo
+    def can_be_assignee?(repo, username)
+      username = user_login(username)
+      github_client.check_assignee(repo, username)
+    end
+
+    # Uses the GitHub API to determine if a user has a pending invitation
+    def is_invited?(repo, username)
+      username = user_login(username).downcase
+      github_client.repository_invitations(repo).any? { |i| i.invitee.login.downcase == username }
+    end
+
+    # Returns the user login (removes the @ from the username)
+    def user_login(username)
+      username.to_s.strip.sub(/^@/, "")
+    end
+
+    # Returns true if the string is a valid GitHub isername (starts with @)
+    def username?(username)
+      username.match?(/\A@/)
+    end
+  end
+end

data/lib/theoj/journal.rb

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+require_relative "journals_data"
+
+module Theoj
+  class Journal
+    attr_accessor :data
+    attr_accessor :doi_prefix
+    attr_accessor :url
+    attr_accessor :name
+    attr_accessor :alias
+    attr_accessor :launch_date
+
+    def initialize(custom_data = {})
+      set_data custom_data
+    end
+
+    def current_year
+      data[:current_year] || Time.new.year
+    end
+
+    def current_volume
+      data[:current_volume] || (Time.new.year - (launch_year - 1))
+    end
+
+    def current_issue
+      data[:current_issue] || (1 + ((Time.new.year * 12 + Time.new.month) - (launch_year * 12 + launch_month)))
+    end
+
+    def paper_id_from_issue(review_issue_id)
+      id = "%05d" % review_issue_id
+      "#{@alias}.#{id}"
+    end
+
+    def paper_doi_for_id(paper_id)
+      "#@doi_prefix/#{paper_id}"
+    end
+
+    def reviews_repository_url(issue_id=nil)
+      reviews_url = "https://github.com/#{data[:reviews_repository]}"
+      if issue_id
+        reviews_url += "/issues/" + issue_id.to_s
+      end
+      reviews_url
+    end
+
+    def year_volume_issue_for_date(d)
+      d = Date.parse(d) if d.is_a? String
+      year = d.year
+      volume = year - (launch_year - 1)
+      issue = (1 + ((year * 12 + d.month) - (launch_year * 12 + launch_month)))
+
+      [year, volume, issue]
+    end
+
+    private
+
+    def set_data(custom_data)
+      @data = default_data.merge(custom_data)
+      @doi_prefix = data[:doi_prefix]
+      @url = data[:url]
+      @name = data[:name]
+      @alias = data[:alias]
+      @launch_date = data[:launch_date]
+    end
+
+    def default_data
+      Theoj::JOURNALS_DATA[:neurolibre]
+    end
+
+    def parsed_launch_date
+      @parsed_launch_date ||= Time.parse(data[:launch_date])
+    end
+
+    def launch_year
+      parsed_launch_date.year
+    end
+
+    def launch_month
+      parsed_launch_date.month
+    end
+  end
+end

data/lib/theoj/journals_data.rb

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+require "date"
+
+module Theoj
+  JOURNALS_DATA = {
+    joss: {
+      doi_prefix: "10.21105",
+      url: "https://joss.theoj.org",
+      name: "Journal of Open Source Software",
+      alias: "joss",
+      launch_date: "2016-05-05",
+      papers_repository: "openjournals/joss-papers",
+      reviews_repository: "openjournals/joss-reviews",
+      deposit_url: "https://joss.theoj.org/papers/api_deposit"
+    },
+    jose: {
+      doi_prefix: "10.21105",
+      url: "https://jose.theoj.org",
+      name: "Journal of Open Source Education",
+      alias: "jose",
+      launch_date: "2018-03-07",
+      papers_repository: "openjournals/jose-papers",
+      reviews_repository: "openjournals/jose-reviews",
+      deposit_url: "https://joss.theoj.org/papers/api_deposit"
+    },
+    jcon: {
+      doi_prefix: "10.21105",
+      url: "https://proceedings.juliacon.org/",
+      name: "The Proceedings of the JuliaCon Conferences",
+      alias: "jcon",
+      launch_date: "2019-07-21",
+      papers_repository: "JuliaCon/proceedings-papers",
+      reviews_repository: "JuliaCon/proceedings-review",
+      deposit_url: "https://proceedings.juliacon.org/papers/api_deposit"
+    },    
+    resciencec: {
+      doi_prefix: "10.21105",
+      url: "https://resciencec.theoj.org",
+      name: "ReScience C",
+      alias: "resciencec",
+      launch_date: "2015-05-23",
+      papers_repository: "ReScience/ReScienceC-papers",
+      reviews_repository: "ReScience/ReScienceC-reviews",
+      deposit_url: "https://resciencec.theoj.org/papers/api_deposit"
+    },
+    neurolibre: {
+      doi_prefix: "10.55458",
+      url: "https://neurolibre.org/",
+      name: "NeuroLibre",
+      alias: "neurolibre",
+      launch_date: "2021-01-01",
+      papers_repository: "neurolibre/preprints",
+      reviews_repository: "neurolibre/neurolibre-reviews",
+      deposit_url: "https://neurolibre-neo.herokuapp.com/papers/api_deposit"
+    },
+    test_journal: {
+      doi_prefix: "10.55458",
+      url: "https://staging.neurolibre.org/",
+      name: "NeuroLibre",
+      alias: "neurolibre",
+      launch_date: "2021-01-01",
+      papers_repository: "neurolibre/neurolibre-preprints-testing",
+      reviews_repository: "openjournals/joss-reviews-testing",
+      deposit_url: "https://staging.neurolibre.org/papers/api_deposit"
+    }
+  }
+end

data/lib/theoj/orcid.rb

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+module Theoj
+  class Orcid
+    attr_reader :orcid, :error
+
+    def initialize(orcid)
+      @orcid = orcid.strip
+      @error = nil
+    end
+
+    def valid?
+      @error = nil
+      return false unless check_structure
+      return false unless check_length
+      return false unless check_chars
+
+      return false unless correct_checksum?
+
+      true
+    end
+
+    def packed_orcid
+      orcid.gsub('-', '')
+    end
+
+    private
+
+    # Returns the last character of the string
+    def checksum_char
+      packed_orcid[-1]
+    end
+
+    def first_11
+      packed_orcid.chop
+    end
+
+    def check_structure
+      groups = orcid.split('-')
+      if groups.size == 4
+        return true
+      else
+        @error = "ORCID looks malformed"
+        return false
+      end
+    end
+
+    def check_length
+      if packed_orcid.length == 16
+        return true
+      else
+        @error = "ORCID looks to be the wrong length"
+        return false
+      end
+    end
+
+    def check_chars
+      valid = true
+      first_11.each_char do |c|
+        if !numeric?(c)
+          @error = "Invalid ORCID digit (#{c})"
+          valid = false
+        end
+      end
+
+      return valid
+    end
+
+    def correct_checksum?
+      validate_against = checksum_char.to_i
+      validate_against = 10 if (checksum_char == "X" || checksum_char == "x")
+
+      if checksum == validate_against
+        return true
+      else
+        @error = "Invalid ORCID"
+        return false
+      end
+    end
+
+    # https://support.orcid.org/knowledgebase/articles/116780-structure-of-the-orcid-identifier
+    def checksum
+      total = 0
+      first_11.each_char do |c|
+        total = (total + c.to_i) * 2
+      end
+
+      remainder = total % 11
+      result = (12 - remainder) % 11
+    end
+
+
+    def numeric?(s)
+      Float(s) != nil rescue false
+    end
+
+  end
+end

data/lib/theoj/paper.rb

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+require "find"
+require "yaml"
+require "rugged"
+require "linguist"
+
+module Theoj
+  class Paper
+    include Theoj::Git
+
+    attr_accessor :review_issue
+    attr_accessor :repository
+    attr_accessor :paper_path
+    attr_accessor :branch
+    attr_accessor :paper_metadata
+
+    def initialize(repository_url, branch, path = nil)
+      @repository = repository_url
+      @branch = branch
+      find_paper path
+      load_metadata
+    end
+
+    def authors
+      @authors ||= parse_authors
+    end
+
+    def citation_author
+      surname = authors.first.last_name
+      initials = authors.first.initials
+
+      if authors.size > 1
+        return "#{surname} et al."
+      else
+        return "#{surname}, #{initials}"
+      end
+    end
+
+    def title
+      @paper_metadata["title"]
+    end
+
+    def tags
+      @paper_metadata["tags"]
+    end
+
+    def date
+      @paper_metadata["date"]
+    end
+
+    def languages
+      @languages ||= detect_languages
+    end
+
+    def bibliography_path
+      @paper_metadata["bibliography"]
+    end
+
+    def local_path
+      @local_path ||= "tmp/#{SecureRandom.hex}"
+    end
+
+    def cleanup
+      FileUtils.rm_rf(local_path) if Dir.exist?(local_path)
+    end
+
+    def self.find_paper_path(search_path)
+      paper_path = nil
+
+      if Dir.exist? search_path
+        Find.find(search_path).each do |path|
+          if path =~ /paper\.tex$|paper\.md$/
+            paper_path = path
+            break
+          end
+        end
+      end
+
+      paper_path
+    end
+
+    def self.from_repo(repository_url, branch = "")
+      Paper.new(repository_url, branch, nil)
+    end
+
+    private
+
+      def find_paper(path)
+        if path.to_s.strip.empty?
+          setup_local_repo
+          @paper_path = Theoj::Paper.find_paper_path(local_path)
+        else
+          @paper_path = path
+        end
+      end
+
+      def setup_local_repo
+        msg_no_repo = "Downloading of the repository failed. Please make sure the URL is correct."
+        msg_no_branch = "Couldn't check the bibtex because branch name is incorrect: #{branch.to_s}"
+
+        error = clone_repo(repository, local_path) ? nil : msg_no_repo
+        (error = change_branch(branch, local_path) ? nil : msg_no_branch) unless error
+
+        failure(error) if error
+        error.nil?
+      end
+
+      def load_metadata
+        @paper_metadata ||= if paper_path.nil?
+          {}
+        elsif paper_path.include?('.tex')
+          YAML.load_file(paper_path.gsub('.tex', '.yml'))
+        else
+          YAML.load_file(paper_path)
+        end
+      end
+
+      def parse_authors
+        parsed_authors = []
+        authors_metadata = @paper_metadata['authors']
+        affiliations_metadata = parse_affiliations(@paper_metadata['affiliations'])
+
+        # Loop through the authors block and build up the affiliation
+        authors_metadata.each do |author|
+          author['name'] = author.dup if author['name'].nil?
+          affiliation_index = author['affiliation']
+          failure "Author (#{author['name']}) is missing affiliation" if affiliation_index.nil?
+          begin
+            parsed_author = Author.new(author['name'], author['orcid'], affiliation_index, affiliations_metadata)
+          rescue Exception => e
+            failure(e.message)
+          end
+          parsed_authors << parsed_author
+        end
+
+        parsed_authors
+      end
+
+      def parse_affiliations(affiliations_yaml)
+        affiliations_metadata = {}
+
+        affiliations_yaml.each do |affiliation|
+          affiliations_metadata[affiliation['index']] = affiliation['name']
+        end
+
+        affiliations_metadata
+      end
+
+      def detect_languages
+        repo = Rugged::Repository.discover(paper_path)
+        project = Linguist::Repository.new(repo, repo.head.target_id)
+
+        # Take top five languages from Linguist
+        project.languages.keys.take(5)
+      end
+
+      def failure(msg)
+        cleanup
+        raise Theoj::Error, msg
+      end
+  end
+end

data/lib/theoj/published_paper.rb

@@ -0,0 +1,46 @@
+require "faraday"
+require "yaml"
+require "json"
+
+module Theoj
+  class PublishedPaper
+    include Theoj::Git
+
+    attr_accessor :metadata
+
+    def initialize(doi)
+      doi_url = "https://doi.org/#{doi}"
+      doi_response = Faraday.get(doi_url)
+      if doi_response.status == 302
+        paper_url = doi_response.headers[:location]
+      else
+        raise Theoj::Error, "The DOI is invalid, url does not resolve #{doi_url}"
+      end
+
+      paper_data = Faraday.get(paper_url + ".json")
+      if paper_data.status == 200
+        @metadata = JSON.parse(paper_data.body, symbolize_names: true)
+      else
+        raise Theoj::Error, "Could not find the paper data at #{paper_url + ".json"}"
+      end
+    end
+
+    [:title, :state, :submitted_at, :doi, :published_at,
+     :volume, :issue, :year, :page, :authors, :editor,
+     :editor_name, :editor_url, :editor_orcid, :reviewers,
+     :languages, :tags, :software_repository, :paper_review,
+     :pdf_url, :software_archive].each do |method_name|
+      define_method(method_name) { metadata[method_name] }
+      define_method("#{method_name}=") {|value| @metadata[method_name] = value }
+    end
+
+    def yaml_metadata
+      metadata.transform_keys(&:to_s).to_yaml
+    end
+
+    def json_metadata
+      metadata.to_json
+    end
+
+  end
+end

data/lib/theoj/review_issue.rb

@@ -0,0 +1,92 @@
+require "securerandom"
+
+module Theoj
+  class ReviewIssue
+    include Theoj::GitHub
+
+    attr_accessor :issue_id
+    attr_accessor :repository
+    attr_accessor :paper
+    attr_accessor :local_path
+
+    def initialize(repository, issue_id, access_token=nil)
+      @issue_id = issue_id
+      @repository = repository
+      @github_access_token = access_token
+    end
+
+    def issue_body
+      @issue_body ||= issue(repository, issue_id).body
+    end
+
+    def paper
+      @paper ||= Theoj::Paper.new(target_repository, paper_branch)
+    end
+
+    def target_repository
+      @target_repository ||= read_value_from_body("target-repository")
+    end
+
+    def reviewers
+      @reviewers ||= read_value_from_body("reviewers-list").split(",").map{|r| r.strip} - ["Pending", "TBD"]
+    end
+
+    def editor
+      @editor ||= read_value_from_body("editor")
+    end
+
+    #@NeuroLibre -- START
+    # Removes @archive, uses the following instead.
+    def book_exec_url
+      @book_exec_url ||= read_value_from_body("book-exec-url")
+    end
+
+    def repository_archive
+      @repository_archive ||= read_value_from_body("repository-archive")
+    end
+
+    def data_archive
+      @data_archive ||= read_value_from_body("data-archive")
+    end
+
+    def book_archive
+      @book_archive ||= read_value_from_body("book-archive")
+    end
+
+    def docker_archive
+      @docker_archive ||= read_value_from_body("docker-archive")
+    end
+    #@NeuroLibre -- END
+
+    def version
+      @version ||= read_value_from_body("version")
+    end
+
+    def paper_branch
+      @paper_branch ||= read_value_from_body("branch")
+    end
+
+    def value_for(value_name)
+      read_value_from_body(value_name)
+    end
+
+    private
+
+      def read_from_body(start_mark, end_mark)
+        text = ""
+        issue_body.match(/#{start_mark}(.*)#{end_mark}/im) do |m|
+          text = m[1]
+        end
+
+        text = "" if ["Pending", "TBD"].include?(text.strip)
+        text.strip
+      end
+
+      # Read value in issue's body between HTML comments
+      def read_value_from_body(value_name)
+        start_mark = "<!--#{value_name}-->"
+        end_mark = "<!--end-#{value_name}-->"
+        read_from_body(start_mark, end_mark)
+      end
+  end
+end

data/lib/theoj/submission.rb

@@ -0,0 +1,233 @@
+require "json"
+require "date"
+require "base64"
+require "faraday"
+require "commonmarker"
+
+module Theoj
+  class Submission
+    include Theoj::GitHub
+
+    attr_accessor :journal
+    attr_accessor :review_issue
+    attr_accessor :paper
+
+    def initialize(journal, review_issue, paper=nil)
+      @journal = journal
+      @review_issue = review_issue
+      @paper = paper || @review_issue.paper
+    end
+
+    # @NeuroLibre -- START
+    # Removes archive_doi, adds neurolibre reproducibility assets DOIs.
+    def deposit_payload
+      {
+        id: metadata_info[:review_issue_id],
+        metadata: Base64.encode64(metadata_payload),
+        doi: metadata_info[:doi],
+        repository_doi: metadata_info[:repository_doi],
+        book_exec_url: metadata_info[:book_exec_url],
+        data_doi: metadata_info[:data_doi],
+        book_doi: metadata_info[:book_doi],
+        docker_doi: metadata_info[:docker_doi],
+        citation_string: citation_string,
+        title: metadata_info[:title]
+      }
+    end
+    # @NeuroLibre -- END
+
+    # Create a metadata json payload
+    # @NeuroLibre -- START
+    # Removes archive_doi, adds neurolibre reproducibility assets DOIs.
+    def metadata_payload
+      {
+        paper: {
+          title: metadata_info[:title],
+          tags: metadata_info[:tags],
+          languages: metadata_info[:languages],
+          authors: metadata_info[:authors],
+          doi: metadata_info[:doi],
+          
+          repository_doi: metadata_info[:repository_doi],
+          book_exec_url: metadata_info[:book_exec_url],
+          data_doi: metadata_info[:data_doi],
+          book_doi: metadata_info[:book_doi],
+          docker_doi: metadata_info[:docker_doi],
+
+          repository_address: metadata_info[:software_repository_url],
+          editor: metadata_info[:review_editor],
+          reviewers: metadata_info[:reviewers].collect(&:strip),
+          volume: metadata_info[:volume],
+          issue: metadata_info[:issue],
+          year: metadata_info[:year],
+          page: metadata_info[:page]
+        }
+      }.to_json
+    end
+    # @NeuroLibre -- END
+
+    # Create metadata used to generate PDF/JATS outputs
+    # @NeuroLibre -- START
+    # Removes archive_doi, adds neurolibre reproducibility assets DOIs.
+    def article_metadata
+      {
+        title: metadata_info[:title],
+        tags: metadata_info[:tags],
+        authors: metadata_info[:authors],
+        doi: metadata_info[:doi],
+        software_repository_url: metadata_info[:software_repository_url],
+        reviewers: metadata_info[:reviewers].collect{|r| user_login(r)},
+        volume: metadata_info[:volume],
+        issue: metadata_info[:issue],
+        year: metadata_info[:year],
+        page: metadata_info[:page],
+        journal_alias: metadata_info[:journal_alias],
+        software_review_url: metadata_info[:software_review_url],
+
+        repository_doi: metadata_info[:repository_doi],
+        book_exec_url: metadata_info[:book_exec_url],
+        data_doi: metadata_info[:data_doi],
+        book_doi: metadata_info[:book_doi],
+        docker_doi: metadata_info[:docker_doi],
+        
+        citation_string: metadata_info[:citation_string],
+        editor: metadata_info[:editor],
+        submitted_at: metadata_info[:submitted_at],
+        published_at: metadata_info[:published_at]
+      }
+    end
+    # @NeuroLibre -- END
+
+    def metadata_info
+      @metadata_info ||= all_metadata
+    end
+
+    def deposit!(secret)
+      parameters = deposit_payload.merge(secret: secret)
+      Faraday.post(journal.data[:deposit_url], parameters.to_json, {"Content-Type" => "application/json"})
+    end
+
+    def citation_string
+      metadata_info[:citation_string]
+    end
+
+    def paper_id
+      journal.paper_id_from_issue(review_issue.issue_id)
+    end
+
+    def paper_doi
+      journal.paper_doi_for_id(paper_id)
+    end
+
+    # @NeuroLibre -- START
+    # Removes archive_doi, adds neurolibre reproducibility assets DOIs.
+    def all_metadata
+      metadata = {
+        title: plaintext(paper.title),
+        tags: paper.tags,
+        languages: paper.languages,
+        authors: paper.authors.collect { |a| a.to_h },
+        doi: paper_doi,
+        software_repository_url: review_issue.target_repository,
+        review_issue_id: review_issue.issue_id,
+        review_editor: review_issue.editor,
+        reviewers: review_issue.reviewers,
+        volume: journal.current_volume,
+        issue: journal.current_issue,
+        year: journal.current_year,
+        page: review_issue.issue_id,
+        journal_alias: journal.alias,
+        journal_name: journal.name,
+        software_review_url: journal.reviews_repository_url(review_issue.issue_id),
+        
+        # Context changes from archive --> doi
+        repository_doi: review_issue.repository_archive,
+        data_doi: review_issue.data_archive,
+        book_doi: review_issue.book_archive,
+        docker_doi: review_issue.docker_archive,
+        # Context does not change for this
+        book_exec_url: review_issue.book_exec_url,
+        
+        citation_author: paper.citation_author
+      }
+      # @NeuroLibre -- END
+
+      metadata.merge!(editor_info, dates_info)
+      metadata[:citation_string] = build_citation_string(metadata)
+      metadata
+    end
+
+    def editor_info
+      editor_info = { editor: {
+                        github_user: user_login(review_issue.editor),
+                        name: nil,
+                        url: nil,
+                        orcid: nil
+                        }
+                    }
+
+      if review_issue.editor
+        editor_lookup = Faraday.get(journal.url + "/editors/lookup/" + user_login(review_issue.editor))
+        if editor_lookup.status == 200
+          info = JSON.parse(editor_lookup.body, symbolize_names: true)
+          editor_info[:editor][:name] = info[:name]
+          editor_info[:editor][:url] = info[:url]
+          editor_info[:editor][:orcid] = info[:orcid]
+        end
+      end
+
+      editor_info
+    end
+
+    def dates_info
+      dates_info = { submitted_at: nil, published_at: nil }
+
+      if review_issue.issue_id
+        paper_lookup = Faraday.get(journal.url + "/papers/lookup/" + review_issue.issue_id.to_s)
+        if paper_lookup.status == 200
+          info = JSON.parse(paper_lookup.body, symbolize_names: true)
+          dates_info[:submitted_at] = format_date(info[:submitted]) if info[:submitted]
+          dates_info[:published_at] = format_date(info[:accepted]) if info[:accepted]
+        end
+
+        if dates_info[:published_at]
+          yvi = journal.year_volume_issue_for_date(Date.parse(dates_info[:published_at]))
+          dates_info[:year] = yvi[0]
+          dates_info[:volume] = yvi[1]
+          dates_info[:issue] = yvi[2]
+        end
+      end
+
+      dates_info
+    end
+
+    def track
+      track_info = { name: nil, short_name: nil, code: nil, label: nil, parameterized: nil}
+
+      if review_issue.issue_id
+        track_lookup = Faraday.get(journal.url + "/papers/" + review_issue.issue_id.to_s + "/lookup_track" )
+        if track_lookup.status == 200
+          track_info = JSON.parse(track_lookup.body, symbolize_names: true)
+        end
+      end
+
+      track_info
+    end
+
+    private
+
+    def build_citation_string(metadata)
+      "#{metadata[:citation_author]}, (#{metadata[:year]}). #{metadata[:title]}. #{metadata[:journal_name]}, #{metadata[:volume]}(#{metadata[:issue]}), #{metadata[:review_issue_id]}, https://doi.org/#{metadata[:doi]}"
+    end
+
+    def plaintext(t)
+      CommonMarker.render_doc(t, :DEFAULT).to_plaintext.strip.gsub(" ", " ").gsub("\n", " ")
+    end
+
+    def format_date(date_string)
+      Date.parse(date_string.to_s).strftime("%Y-%m-%d")
+    rescue Date::Error
+      nil
+    end
+  end
+end

data/lib/theoj/version.rb

@@ -0,0 +1,3 @@
+module Theoj
+  VERSION = "1.5.3"
+end

metadata

@@ -0,0 +1,192 @@
+--- !ruby/object:Gem::Specification
+name: neurolibre
+version: !ruby/object:Gem::Version
+  version: 1.5.3
+platform: ruby
+authors:
+- Juanjo Bazán
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2023-04-24 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: octokit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '6.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '6.0'
+- !ruby/object:Gem::Dependency
+  name: faraday
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.7'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.7'
+- !ruby/object:Gem::Dependency
+  name: faraday-retry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: openjournals-nameable
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+- !ruby/object:Gem::Dependency
+  name: github-linguist
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '7.24'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '7.24'
+- !ruby/object:Gem::Dependency
+  name: rugged
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: commonmarker
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.23'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.23'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 13.0.6
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 13.0.6
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.11'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.11'
+description: A library to manage editorial objects used in the NeuroLibre's moderation
+  and screening process
+email:
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- CHANGELOG.md
+- LICENSE
+- README.md
+- lib/neurolibre.rb
+- lib/theoj/author.rb
+- lib/theoj/git.rb
+- lib/theoj/github.rb
+- lib/theoj/journal.rb
+- lib/theoj/journals_data.rb
+- lib/theoj/orcid.rb
+- lib/theoj/paper.rb
+- lib/theoj/published_paper.rb
+- lib/theoj/review_issue.rb
+- lib/theoj/submission.rb
+- lib/theoj/version.rb
+homepage: http://github.com/neurolibre/neurolibre-gem
+licenses:
+- MIT
+metadata:
+  bug_tracker_uri: https://github.com/neurolibre/neurolibre-gem/issues
+  changelog_uri: https://github.com/neurolibre/neurolibre-gem/blob/main/CHANGELOG.md
+  documentation_uri: https://www.rubydoc.info/gems/neurolibre
+  homepage_uri: http://github.com/neurolibre/neurolibre-gem
+  source_code_uri: http://github.com/neurolibre/neurolibre-gem
+post_install_message:
+rdoc_options:
+- "--main"
+- README.md
+- "--charset=UTF-8"
+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: 3.4.6
+signing_key:
+specification_version: 4
+summary: Editorial objects used by NeuroLibre
+test_files: []