niso-jats 0.1.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 1fd350063689f53905bba191ec517842f877f5504b501d71973557ece6aeffd3
+  data.tar.gz: bfb960f193a69eea2331feeafab8282e9d72e9cb9e0c6454684791907e7d6f40
+SHA512:
+  metadata.gz: afe4dd257d5fe4a3aa404bdf5e50b7762934d966c75028e8eb0e08b082d16a0c167f525cfce5d5dcbe7c780d1aab7f25e3868f42de2a28a895cf64b42477c706
+  data.tar.gz: dad120c624972f93e69eb9aa948a8e65a68b99a442c6027fd04b2a50ea15cf83d586014ecdcafe2f75c6ab8fa4a15d7c4cbc58837d0b1a24ca640b081916a3ff

data/.github/workflows/rake.yml

@@ -0,0 +1,18 @@
+# Auto-generated by Cimas: Do not edit it manually!
+# See https://github.com/metanorma/cimas
+name: rake
+
+on:
+  push:
+    branches: [ master, main ]
+    tags: [ v* ]
+  pull_request:
+
+permissions:
+  contents: write
+
+jobs:
+  rake:
+    uses: metanorma/ci/.github/workflows/generic-rake.yml@main
+    secrets:
+      pat_token: ${{ secrets.METANORMA_CI_PAT_TOKEN }}

data/.github/workflows/release.yml

@@ -0,0 +1,25 @@
+# Auto-generated by Cimas: Do not edit it manually!
+# See https://github.com/metanorma/cimas
+name: release
+
+on:
+  workflow_dispatch:
+    inputs:
+      next_version:
+        description: |
+          Next release version. Possible values: x.y.z, major, minor, patch (or pre|rc|etc).
+          Also, you can pass 'skip' to skip 'git tag' and do 'gem push' for the current version
+        required: true
+        default: 'skip'
+  repository_dispatch:
+    types: [ do-release ]
+
+jobs:
+  release:
+    uses: metanorma/ci/.github/workflows/rubygems-release.yml@main
+    with:
+      next_version: ${{ github.event.inputs.next_version }}
+    secrets:
+      rubygems-api-key: ${{ secrets.METANORMA_CI_RUBYGEMS_API_KEY }}
+      pat_token: ${{ secrets.METANORMA_CI_PAT_TOKEN }}
+

data/.gitignore

@@ -0,0 +1,13 @@
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status
+Gemfile.lock
+.rubocop-https---raw-githubusercontent-com-riboseinc-oss-guides-master-ci-rubocop-yml

data/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "spec/fixtures/niso-jats"]
+	path = spec/fixtures/niso-jats
+	url = git@github.com:ncbi/niso-jats.git

data/.rspec

@@ -0,0 +1,3 @@
+--format documentation
+--color
+--require spec_helper

data/.rubocop.yml

@@ -0,0 +1,21 @@
+# Auto-generated by Cimas: Do not edit it manually!
+# See https://github.com/metanorma/cimas
+inherit_from:
+  - https://raw.githubusercontent.com/riboseinc/oss-guides/master/ci/rubocop.yml
+
+Metrics/BlockLength:
+  Enabled: false
+
+Metrics/MethodLength:
+  Enabled: false
+
+Metrics/AbcSize:
+  Enabled: false
+
+Layout/LineLength:
+  Max: 120
+
+AllCops:
+  TargetRubyVersion: 3.0
+  SuggestExtensions: false
+  NewCops: enable

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,84 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at ronald.tse@ribose.com. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior,  harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

data/Gemfile

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+# Specify your gem's dependencies in niso-jats.gemspec
+gemspec
+
+gem "equivalent-xml"
+gem "pry"
+gem "rake", "~> 13.0"
+gem "rspec", "~> 3.11"
+gem "rubocop", "~> 1.58"
+gem "rubocop-performance", "~> 1.21", ">= 1.21.1"
+gem "xml-c14n"

data/README.adoc

@@ -0,0 +1,73 @@
+= NISO JATS Ruby library
+
+The `niso-jats` library is a parser and generator for NISO JATS XML documents.
+
+It is intended to be used to parse and generate NISO JATS XML v1.2 documents.
+
+== Installation
+
+Add this line to your application's Gemfile:
+
+[source,ruby]
+----
+gem 'niso-jats'
+----
+
+And then execute:
+
+[source]
+----
+$ bundle install
+----
+
+Or install it yourself as:
+
+[source]
+----
+$ gem install niso-jats
+----
+
+
+== Usage
+
+To parse a NISO JATS XML document:
+
+[source,ruby]
+----
+require 'niso-jats'
+
+jats = NisoJats::Document.new(File.read('jats.xml'))
+puts jats.title
+puts jats.abstract
+puts jats.sections
+----
+
+To generate a NISO JATS XML document:
+
+[source,ruby]
+----
+require 'niso-jats'
+
+jats = NisoJats::Document.new
+jats.title = 'An Article Title'
+jats.abstract = 'An Article Abstract'
+jats.sections = [
+  NisoJats::Section.new('Section 1', 'This is the first section'),
+  NisoJats::Section.new('Section 2', 'This is the second section')
+]
+
+puts jats.to_xml
+----
+
+
+== Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/metanorma/niso-jats.
+
+
+== Copyright and license
+
+The gem is available as open source under the terms of the BSD 2-clause license.
+
+All rights reserved. Ribose
+

data/Rakefile

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+require "rubocop/rake_task"
+
+RuboCop::RakeTask.new
+
+task default: %i[spec rubocop]

data/bin/console

@@ -0,0 +1,11 @@
+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require "bundler/setup"
+require "niso/jats"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/niso/jats/abbrev.rb

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+module Niso
+  module Jats
+    class Abbrev < Lutaml::Model::Serializable
+      attribute :content, :string
+      attribute :alt, :string
+      attribute :content_type, :string
+      attribute :hreflang, :string
+      attribute :id, :string
+      attribute :specific_use, :string
+      attribute :lang, :string
+      attribute :def, Def, collection: true
+
+      xml do
+        root "abbrev"
+
+        map_content to: :content
+        map_attribute "alt", to: :alt
+        map_attribute "content-type", to: :content_type
+        map_attribute "hreflang", to: :hreflang
+        map_attribute "id", to: :id
+        map_attribute "specific-use", to: :specific_use
+        map_attribute "lang", to: :lang, namespace: "http://www.w3.org/XML/1998/namespace", prefix: "xml"
+        map_element "def", to: :def
+      end
+    end
+  end
+end

data/lib/niso/jats/abbrev_journal_title.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+module Niso
+  module Jats
+    class AbbrevJournalTitle < Lutaml::Model::Serializable
+      attribute :content, :string
+      attribute :abbrev_type, :string
+      attribute :id, :string
+      attribute :specific_use, :string
+      attribute :lang, :string
+
+      xml do
+        root "abbrev-journal-title"
+
+        map_content to: :content
+        map_attribute "abbrev-type", to: :abbrev_type
+        map_attribute "id", to: :id
+        map_attribute "specific-use", to: :specific_use
+        map_attribute "lang", to: :lang, namespace: "http://www.w3.org/XML/1998/namespace", prefix: "xml"
+      end
+    end
+  end
+end

data/lib/niso/jats/abstract.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Niso
+  module Jats
+    class Abstract < Lutaml::Model::Serializable
+      attribute :abstract_type, :string
+      attribute :id, :string
+      attribute :specific_use, :string
+      attribute :lang, :string
+      attribute :object_id, ObjectId, collection: true
+      attribute :label, Label
+      attribute :title, Title
+      attribute :p, Paragraph, collection: true
+      attribute :sec, Sec, collection: true
+
+      xml do
+        root "abstract"
+
+        map_attribute "abstract-type", to: :abstract_type
+        map_attribute "id", to: :id
+        map_attribute "specific-use", to: :specific_use
+        map_attribute "lang", to: :lang, namespace: "http://www.w3.org/XML/1998/namespace", prefix: "xml"
+        map_element "object-id", to: :object_id
+        map_element "label", to: :label
+        map_element "title", to: :title
+        map_element "p", to: :p
+        map_element "sec", to: :sec
+      end
+    end
+  end
+end

data/lib/niso/jats/access_date.rb

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+module Niso
+  module Jats
+    class AccessDate < Lutaml::Model::Serializable
+      attribute :content, :string
+      attribute :calendar, :string
+      attribute :content_type, :string
+      attribute :id, :string
+      attribute :iso_8601_date, :string
+      attribute :specific_use, :string
+
+      xml do
+        root "access-date"
+
+        map_content to: :content
+        map_attribute "calendar", to: :calendar
+        map_attribute "content-type", to: :content_type
+        map_attribute "id", to: :id
+        map_attribute "iso-8601-date", to: :iso_8601_date
+        map_attribute "specific-use", to: :specific_use
+      end
+    end
+  end
+end

data/lib/niso/jats/ack.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+module Niso
+  module Jats
+    class Ack < Lutaml::Model::Serializable
+      attribute :content_type, :string
+      attribute :id, :string
+      attribute :specific_use, :string
+      attribute :lang, :string
+      attribute :object_id, ObjectId, collection: true
+      attribute :label, Label
+      attribute :title, Title
+      attribute :abstract, Abstract, collection: true
+      attribute :kwd_group, KwdGroup, collection: true
+      attribute :subj_group, SubjGroup, collection: true
+      attribute :p, Paragraph, collection: true
+      attribute :sec, Sec, collection: true
+      attribute :ref_list, RefList, collection: true
+
+      xml do
+        root "ack"
+
+        map_attribute "content-type", to: :content_type
+        map_attribute "id", to: :id
+        map_attribute "specific-use", to: :specific_use
+        map_attribute "lang", to: :lang, namespace: "http://www.w3.org/XML/1998/namespace", prefix: "xml"
+        map_element "object-id", to: :object_id
+        map_element "label", to: :label
+        map_element "title", to: :title
+        map_element "abstract", to: :abstract
+        map_element "kwd-group", to: :kwd_group
+        map_element "subj-group", to: :subj_group
+        map_element "p", to: :p
+        map_element "sec", to: :sec
+        map_element "ref-list", to: :ref_list
+      end
+    end
+  end
+end

data/lib/niso/jats/addr_line.rb

@@ -0,0 +1,91 @@
+# frozen_string_literal: true
+
+module Niso
+  module Jats
+    class AddrLine < Lutaml::Model::Serializable
+      attribute :content, :string
+      attribute :content_type, :string
+      attribute :id, :string
+      attribute :specific_use, :string
+      attribute :lang, :string
+      attribute :bold, Bold, collection: true
+      attribute :fixed_case, FixedCase, collection: true
+      attribute :italic, Italic, collection: true
+      attribute :monospace, Monospace, collection: true
+      attribute :overline, Overline, collection: true
+      attribute :roman, Roman, collection: true
+      attribute :sans_serif, SansSerif, collection: true
+      attribute :sc, Sc, collection: true
+      attribute :strike, Strike, collection: true
+      attribute :underline, Underline, collection: true
+      attribute :ruby, Ruby, collection: true
+      attribute :alternatives, Alternatives, collection: true
+      attribute :inline_graphic, InlineGraphic, collection: true
+      attribute :inline_media, InlineMedia, collection: true
+      attribute :private_char, PrivateChar, collection: true
+      attribute :chem_struct, ChemStruct, collection: true
+      attribute :inline_formula, InlineFormula, collection: true
+      attribute :abbrev, Abbrev, collection: true
+      attribute :index_term, IndexTerm, collection: true
+      attribute :index_term_range_end, IndexTermRangeEnd, collection: true
+      attribute :milestone_end, MilestoneEnd, collection: true
+      attribute :milestone_start, MilestoneStart, collection: true
+      attribute :named_content, NamedContent, collection: true
+      attribute :styled_content, StyledContent, collection: true
+      attribute :sub, Sub, collection: true
+      attribute :sup, Sup, collection: true
+      attribute :city, City, collection: true
+      attribute :country, Country, collection: true
+      attribute :fax, Fax, collection: true
+      attribute :institution, Institution, collection: true
+      attribute :institution_wrap, InstitutionWrap, collection: true
+      attribute :phone, Phone, collection: true
+      attribute :postal_code, PostalCode, collection: true
+      attribute :state, State, collection: true
+
+      xml do
+        root "addr-line"
+
+        map_content to: :content
+        map_attribute "content-type", to: :content_type
+        map_attribute "id", to: :id
+        map_attribute "specific-use", to: :specific_use
+        map_attribute "lang", to: :lang, namespace: "http://www.w3.org/XML/1998/namespace", prefix: "xml"
+        map_element "bold", to: :bold
+        map_element "fixed-case", to: :fixed_case
+        map_element "italic", to: :italic
+        map_element "monospace", to: :monospace
+        map_element "overline", to: :overline
+        map_element "roman", to: :roman
+        map_element "sans-serif", to: :sans_serif
+        map_element "sc", to: :sc
+        map_element "strike", to: :strike
+        map_element "underline", to: :underline
+        map_element "ruby", to: :ruby
+        map_element "alternatives", to: :alternatives
+        map_element "inline-graphic", to: :inline_graphic
+        map_element "inline-media", to: :inline_media
+        map_element "private-char", to: :private_char
+        map_element "chem-struct", to: :chem_struct
+        map_element "inline-formula", to: :inline_formula
+        map_element "abbrev", to: :abbrev
+        map_element "index-term", to: :index_term
+        map_element "index-term-range-end", to: :index_term_range_end
+        map_element "milestone-end", to: :milestone_end
+        map_element "milestone-start", to: :milestone_start
+        map_element "named-content", to: :named_content
+        map_element "styled-content", to: :styled_content
+        map_element "sub", to: :sub
+        map_element "sup", to: :sup
+        map_element "city", to: :city
+        map_element "country", to: :country
+        map_element "fax", to: :fax
+        map_element "institution", to: :institution
+        map_element "institution-wrap", to: :institution_wrap
+        map_element "phone", to: :phone
+        map_element "postal-code", to: :postal_code
+        map_element "state", to: :state
+      end
+    end
+  end
+end

data/lib/niso/jats/address.rb

@@ -0,0 +1,45 @@
+# frozen_string_literal: true
+
+module Niso
+  module Jats
+    class Address < Lutaml::Model::Serializable
+      attribute :content_type, :string
+      attribute :id, :string
+      attribute :specific_use, :string
+      attribute :lang, :string
+      attribute :addr_line, AddrLine, collection: true
+      attribute :city, City, collection: true
+      attribute :country, Country, collection: true
+      attribute :fax, Fax, collection: true
+      attribute :institution, Institution, collection: true
+      attribute :institution_wrap, InstitutionWrap, collection: true
+      attribute :phone, Phone, collection: true
+      attribute :postal_code, PostalCode, collection: true
+      attribute :state, State, collection: true
+      attribute :email, Email, collection: true
+      attribute :ext_link, ExtLink, collection: true
+      attribute :uri, Uri, collection: true
+
+      xml do
+        root "address"
+
+        map_attribute "content-type", to: :content_type
+        map_attribute "id", to: :id
+        map_attribute "specific-use", to: :specific_use
+        map_attribute "lang", to: :lang, namespace: "http://www.w3.org/XML/1998/namespace", prefix: "xml"
+        map_element "addr-line", to: :addr_line
+        map_element "city", to: :city
+        map_element "country", to: :country
+        map_element "fax", to: :fax
+        map_element "institution", to: :institution
+        map_element "institution-wrap", to: :institution_wrap
+        map_element "phone", to: :phone
+        map_element "postal-code", to: :postal_code
+        map_element "state", to: :state
+        map_element "email", to: :email
+        map_element "ext-link", to: :ext_link
+        map_element "uri", to: :uri
+      end
+    end
+  end
+end