plazucchini 0.0.1

checksums.yaml

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data/.github/workflows/main.yaml

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+name: Ruby
+
+on: [push,pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: 3.3.4
+        bundler-cache: true
+    - name: Run the default task
+      run: bundle exec rake

data/.gitignore

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+.byebug_history
+.vscode
+.idea
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+*.gem
+Gemfile.lock

data/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.0.1] - 2026-01-27
+
+### Added
+- Initial release
+- Plazi API wrapper based on checkerberry structure
+- TreatmentsForTaxon endpoint
+- Fetch treatment endpoint

data/CODE_OF_CONDUCT.md

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+# 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 diapriid@gmail.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

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+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+# Specify your gem's dependencies in plazucchini.gemspec
+gemspec
+
+gem "rake", "~> 13.0"
+
+gem "minitest", "~> 5.0"

data/LICENSE

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+The MIT License (MIT)
+
+Copyright © 2024 Species File Group
+
+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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+# Plazucchini
+
+Plazucchini is a Ruby wrapper on the [Plazi's TreatmentBank](https://api.plazi.org) API. Code follows the spirit/approach of the Gem [serrano](https://github.com/sckott/serrano), and indeed much of the wrapping utility is copied 1:1 from that repo, thanks [@sckott](https://github.com/sckott).
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'plazucchini'
+```
+
+And then execute:
+
+    $ bundle install
+
+Or install it yourself as:
+
+    $ gem install plazucchini
+
+## Usage
+
+All Plazi API endpoints are wrapped. Please see the tests for usage examples. Here are a few examples:
+
+### [Search by DOI](http://api.plazi.org/GgSrvApi/v1#Treatments.searchByDOI)
+
+Get treatments for a taxon:
+```ruby
+Plazucchini.treatments_search_by_doi(doi: '10.5281/zenodo.8117062', limit: 1)
+```
+
+### [Treatments for Taxon](http://api.plazi.org/GgSrvApi/v1#Treatments.fetch)
+
+Get treatments for a taxon:
+```ruby
+Plazucchini.treatments_for_taxon(genus: 'Arboridia', species: 'septempunctata', limit: 1)
+```
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake test` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, update the CHANGELOG.md, and then run bundle exec rake release, which will create a git tag for the version, push git commits and the created tag, and push the .gem file to rubygems.org.
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/SpeciesFileGroup/plazucchini. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [code of conduct](https://github.com/SpeciesFileGroup/plazucchini/blob/main/CODE_OF_CONDUCT.md).
+
+## License
+
+The gem is available as open source under the terms of the [MIT license](https://github.com/SpeciesFileGroup/plazucchini/blob/main/LICENSE.txt). You can learn more about the MIT license on [Wikipedia](https://en.wikipedia.org/wiki/MIT_License) and compare it with other open source licenses at the [Open Source Initiative](https://opensource.org/license/mit/).
+
+## Code of Conduct
+
+Everyone interacting in the Plazucchini project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/SpeciesFileGroup/plazucchini/blob/main/CODE_OF_CONDUCT.md).

data/Rakefile

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+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList["test/**/*_test.rb"]
+  t.verbose = true
+end
+
+desc "Run tests"
+task default: :test

data/bin/console

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+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require "bundler/setup"
+require "plazucchini"
+
+# 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.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/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/plazucchini/error.rb

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+# frozen_string_literal: true
+
+module Plazucchini
+  class Error < StandardError; end
+  class RequestError < Error; end
+  class Unauthorized < Error; end
+  class NotFound < Error; end
+  class InternalServerError < Error; end
+  class BadGateway < Error; end
+  class ServiceUnavailable < Error; end
+end

data/lib/plazucchini/faraday.rb

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+# frozen_string_literal: true
+
+require "faraday"
+
+module Faraday
+  class PlazucchiniErrors < Faraday::Middleware
+    def on_complete(env)
+      @env = env
+      case env[:status]
+      when 400
+        raise Plazucchini::RequestError, error_message
+      when 401
+        raise Plazucchini::Unauthorized, error_message
+      when 404
+        raise Plazucchini::NotFound, error_message
+      when 500
+        raise Plazucchini::InternalServerError, error_message
+      when 502
+        raise Plazucchini::BadGateway, error_message
+      when 503
+        raise Plazucchini::ServiceUnavailable, error_message
+      end
+    end
+
+    def error_message
+      "#{@env[:method].to_s.upcase} #{@env[:url]}: #{@env[:status]} - #{@env[:body]}"
+    end
+
+    class Middleware < PlazucchiniErrors
+    end
+  end
+end

data/lib/plazucchini/helpers/configuration.rb

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+# taken from https://raw.githubusercontent.com/sckott/serrano/main/lib/serrano/helpers/configuration.rb
+# taken from: https://viget.com/extend/easy-gem-configuration-variables-with-defaults
+module Configuration
+  def configuration
+    yield self
+  end
+
+  def define_setting(name, default = nil)
+    class_variable_set("@@#{name}", default)
+    define_class_method "#{name}=" do |value|
+      class_variable_set("@@#{name}", value)
+    end
+    define_class_method name do
+      class_variable_get("@@#{name}")
+    end
+  end
+
+  private
+
+  def define_class_method(name, &block)
+    (class << self; self; end).instance_eval do
+      define_method name, &block
+    end
+  end
+end

data/lib/plazucchini/request.rb

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+require_relative "faraday"
+require "faraday/follow_redirects"
+require_relative "utils"
+require_relative "xml_parser"
+require "plazucchini/error"
+require "multi_json"
+
+module Plazucchini
+  class Request
+    include Utils
+    attr_accessor :endpoint, :verbose
+
+    def initialize(**args)
+      @endpoint = args[:endpoint]
+      @verbose = args[:verbose]
+      @method = args[:method] || :get
+      @format = args[:format] || :json
+      @limit = args[:limit]
+      @order_mode = args[:order_mode]
+      @author = args[:author]
+      @collector = args[:collector]
+      @doi = args[:doi]
+      @uuid = args[:uuid]
+      @user = args[:user]
+      @status = args[:status]
+      @collection_code = args[:collection_code]
+      @journal = args[:journal]
+      @kingdom_epithet = args[:kingdom_epithet]
+      @phylum_epithet = args[:phylum_epithet]
+      @class_epithet = args[:class_epithet]
+      @order_epithet = args[:order_epithet]
+      @family_epithet = args[:family_epithet]
+      @genus_epithet = args[:genus_epithet]
+      @species_epithet = args[:species_epithet]
+    end
+
+    def perform
+      args = {
+        limit: @limit,
+        orderMode: @order_mode,
+        DOI: @doi,
+        UUID: @uuid,
+        author: @author,
+        collector: @collector,
+        user: @user,
+        status: @status,
+        collectionCode: @collection_code,
+        journal: @journal,
+        kingdom: @kingdom_epithet,
+        phylum: @phylum_epithet,
+        class: @class_epithet,
+        order: @order_epithet,
+        family: @family_epithet,
+        genus: @genus_epithet,
+        species: @species_epithet
+      }
+      # Only include format param for JSON (XML endpoints don't accept format param)
+      args[:format] = @format if @format == :json
+      opts = args.delete_if { |_k, v| v.nil? }
+
+      conn = Faraday.new(url: Plazucchini.base_url) do |f|
+        f.request :json
+        f.response :logger if @verbose
+        f.use Faraday::PlazucchiniErrors::Middleware
+        f.adapter Faraday.default_adapter
+      end
+
+      conn.headers['Accept'] = @format == :xml ? 'application/xml' : 'application/json'
+      conn.headers['Content-Type'] = 'application/json' if @method == :post
+      conn.headers[:user_agent] = make_user_agent
+      conn.headers["X-USER-AGENT"] = make_user_agent
+
+      res = if @method == :post
+              conn.post(endpoint, opts.to_json)
+            else
+              conn.get(endpoint, opts)
+            end
+
+      parse_response(res.body)
+    end
+
+    private
+
+    def parse_response(body)
+      if @format == :xml
+        XmlParser.parse(body)
+      else
+        begin
+          deep_transform_keys(MultiJson.load(body))
+        rescue MultiJson::ParseError
+          body
+        end
+      end
+    end
+  end
+end

data/lib/plazucchini/utils.rb

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+# frozen_string_literal: true
+
+module Plazucchini
+  module Utils
+    def make_user_agent
+      requa = "Faraday/v" + Faraday::VERSION
+      habua = "Plazucchini/v" + Plazucchini::VERSION
+      if Plazucchini.mailto
+        mailto = "mailto:" + Plazucchini.mailto
+        ua = requa + " " + habua + " " + mailto
+      else
+        ua = requa + " " + habua
+      end
+      ua
+    end
+
+    def to_snake_case(str)
+      str.to_s
+         .gsub(/([A-Z]+)([A-Z][a-z])/, '\1_\2')
+         .gsub(/([a-z\d])([A-Z])/, '\1_\2')
+         .gsub(/[-.]/, '_')
+         .downcase
+    end
+
+    def deep_transform_keys(obj)
+      case obj
+      when Hash
+        obj.each_with_object({}) do |(key, value), result|
+          result[to_snake_case(key)] = deep_transform_keys(value)
+        end
+      when Array
+        obj.map { |item| deep_transform_keys(item) }
+      else
+        obj
+      end
+    end
+  end
+end

data/lib/plazucchini/version.rb

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+# frozen_string_literal: true
+
+module Plazucchini
+  VERSION = "0.0.1"
+end

data/lib/plazucchini/xml_parser.rb

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+# frozen_string_literal: true
+
+require "nokogiri"
+require_relative "utils"
+
+module Plazucchini
+  module XmlParser
+    class << self
+      include Utils
+
+      def parse(xml_string)
+        doc = Nokogiri::XML(xml_string)
+        doc.remove_namespaces!
+        node_to_hash(doc.root)
+      end
+
+      private
+
+      def node_to_hash(node)
+        return nil if node.nil?
+
+        result = {}
+
+        # Add attributes with snake_case keys
+        node.attributes.each do |name, attr|
+          result[to_snake_case(name)] = attr.value
+        end
+
+        # Group child elements by name
+        children_by_name = {}
+        node.element_children.each do |child|
+          name = to_snake_case(child.name)
+          children_by_name[name] ||= []
+          children_by_name[name] << child
+        end
+
+        # Process child elements
+        children_by_name.each do |name, children|
+          if children.length == 1
+            result[name] = node_to_hash(children.first)
+          else
+            result[name] = children.map { |child| node_to_hash(child) }
+          end
+        end
+
+        # Handle text content
+        text = node.children.select(&:text?).map(&:text).join.strip
+        if text.length > 0
+          if result.empty?
+            return text
+          else
+            result["text"] = text unless text.empty?
+          end
+        end
+
+        result.empty? ? nil : result
+      end
+    end
+  end
+end