taxa 0.1.0

checksums.yaml

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data/.gitignore

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+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/.rubocop.yml

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+Metrics/MethodLength:
+  Max: 50
+
+AllCops:
+  NewCops: enable

data/.travis.yml

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+---
+language: ruby
+cache: bundler
+rvm:
+  - 2.7.2
+before_install: gem install bundler -v 2.1.4

data/CHANGELOG.md

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+nothing yet

data/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers 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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at shane.sherman@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [https://contributor-covenant.org/version/1/4][version]
+
+[homepage]: https://contributor-covenant.org
+[version]: https://contributor-covenant.org/version/1/4/

data/Gemfile

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+# frozen_string_literal: true
+
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in taxa.gemspec
+gemspec
+
+gem 'minitest', '~> 5.0'
+gem 'rake', '~> 12.0'

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    taxa (0.1.0)
+      faraday (~> 1.1)
+      json (~> 1.8)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    ast (2.4.1)
+    faraday (1.1.0)
+      multipart-post (>= 1.2, < 3)
+      ruby2_keywords
+    json (1.8.6)
+    minitest (5.14.2)
+    multipart-post (2.1.1)
+    parallel (1.20.1)
+    parser (2.7.2.0)
+      ast (~> 2.4.1)
+    rainbow (3.0.0)
+    rake (12.3.3)
+    regexp_parser (2.0.0)
+    rexml (3.2.4)
+    rubocop (1.6.1)
+      parallel (~> 1.10)
+      parser (>= 2.7.1.5)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.8, < 3.0)
+      rexml
+      rubocop-ast (>= 1.2.0, < 2.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 1.4.0, < 2.0)
+    rubocop-ast (1.3.0)
+      parser (>= 2.7.1.5)
+    ruby-progressbar (1.10.1)
+    ruby2_keywords (0.0.2)
+    unicode-display_width (1.7.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  minitest (~> 5.0)
+  rake (~> 12.0)
+  rubocop (~> 1.6)
+  taxa!
+
+BUNDLED WITH
+   2.1.4

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2020 Shane Sherman
+
+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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+# Taxa
+
+Taxa allows users to search multiple taxonomic data sources. Currently only Open Tree of Life is implemented.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'taxa'
+```
+
+And then execute:
+
+    $ bundle install
+
+Or install it yourself as:
+
+    $ gem install taxa
+
+## Usage
+
+client = Taxa::OpenTreeOfLife::Client.new
+
+## 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`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/ssherman/taxa. 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/ssherman/taxa/blob/master/CODE_OF_CONDUCT.md).
+
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+## Code of Conduct
+
+Everyone interacting in the Taxa project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/ssherman/taxa/blob/master/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']
+end
+
+task default: :test

data/bin/console

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+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require 'bundler/setup'
+require 'taxa'
+
+# 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/taxa.rb

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+# frozen_string_literal: true
+
+require 'taxa/version'
+require_relative './taxa/open_tree_of_life/client'
+
+module Taxa
+  # include OpenTreeOfLife
+  class Error < StandardError; end
+  # Your code goes here...
+end

data/lib/taxa/open_tree_of_life/client.rb

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+# frozen_string_literal: true
+
+require_relative './tnrs/base'
+require_relative './tree_of_life/base'
+require_relative './taxonomy/base'
+require_relative './studies/base'
+require 'faraday'
+
+module Taxa
+  module OpenTreeOfLife
+    # API client for Open Tree of Life
+    class Client
+      attr_accessor :options
+      attr_reader :tnrs, :tree_of_life, :taxonomy, :studies
+
+      def initialize(**options)
+        @options = options
+
+        http_client = options[:http_client] || Faraday.new
+        @tnrs = TNRS.new(http_client)
+        @tree_of_life = TreeOfLife.new(http_client)
+        @taxonomy = Taxonomy.new(http_client)
+        @studies = Studies.new(http_client)
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/label_format_helper.rb

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+# frozen_string_literal: true
+
+module Taxa
+  module OpenTreeOfLife
+    # helper module to get label format from parameters
+    module LabelFormatHelper
+      SUBTREE_LABEL_FORMATS = %w[name id name_and_id].freeze
+
+      def get_label_format(format, **parameters)
+        if format == 'newick'
+          label_format = parameters[:label_format] || 'name_and_id'
+          unless SUBTREE_LABEL_FORMATS.include?(label_format)
+            raise ArgumentError, "label_format be one of the following #{SUBTREE_LABEL_FORMATS.join(', ')}"
+          end
+
+          return label_format
+        end
+        nil
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/studies/base.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require_relative './find_studies'
+require_relative './find_trees'
+require_relative './properties'
+require_relative './study'
+require_relative './tree'
+
+module Taxa
+  module OpenTreeOfLife
+    # Studies api endpoints
+    class Studies
+      attr_reader :http_client
+
+      include FindStudies
+      include FindTrees
+      include Properties
+      include Study
+      include Tree
+
+      def initialize(http_client)
+        @http_client = http_client
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/studies/find_studies.rb

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+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Studies
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module FindStudies
+        def find_studies(**parameters)
+          url = 'https://api.opentreeoflife.org/v3/studies/find_studies'
+          response = @http_client.post(url, JSON.generate(parameters),
+                                       'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/studies/find_trees.rb

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+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Studies
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module FindTrees
+        def find_trees(**parameters)
+          url = 'https://api.opentreeoflife.org/v3/studies/find_trees'
+          response = @http_client.post(url, JSON.generate(parameters),
+                                       'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/studies/properties.rb

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+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Studies
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module Properties
+        def properties
+          url = 'https://api.opentreeoflife.org/v3/studies/properties'
+          response = @http_client.post(url, nil, 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/studies/study.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Studies
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module Study
+        def study(id)
+          url = "https://api.opentreeoflife.org/v3/study/#{id}"
+          response = @http_client.get(url, nil, 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/studies/tree.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Studies
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module Tree
+        def tree(study_id, tree_id)
+          url = "https://api.opentreeoflife.org/v3/study/#{study_id}/tree/#{tree_id}"
+          response = @http_client.get(url, nil, 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/taxonomy/about.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Taxonomy
+      # tree of life about api endpoint
+      module About
+        def about
+          response = @http_client.post('https://api.opentreeoflife.org/v3/taxonomy/about')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/taxonomy/base.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require_relative './about'
+require_relative './taxon_info'
+require_relative './mrca'
+require_relative './subtree'
+require_relative '../label_format_helper'
+
+module Taxa
+  module OpenTreeOfLife
+    # Taxonomy api endpoints
+    class Taxonomy
+      include About
+      include TaxonInfo
+      include Mrca
+      include Subtree
+      include LabelFormatHelper
+
+      attr_reader :http_client
+
+      def initialize(http_client)
+        @http_client = http_client
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/taxonomy/mrca.rb

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Taxonomy
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module Mrca
+        def mrca(ott_ids)
+          raise ArgumentError, 'ott_ids required' if ott_ids.nil?
+          raise ArgumentError, 'ott_ids expected to be an array' unless ott_ids.is_a?(Array)
+
+          url = 'https://api.opentreeoflife.org/v3/taxonomy/mrca'
+          response = @http_client.post(url, JSON.generate({ ott_ids: ott_ids }), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/taxonomy/subtree.rb

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Taxonomy
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module Subtree
+        def subtree(**parameters)
+          ott_id = parameters[:ott_id]
+          raise ArgumentError, 'ott_id required' if ott_id.nil?
+
+          label_format = get_label_format('newick', **parameters)
+
+          url = 'https://api.opentreeoflife.org/v3/taxonomy/subtree'
+          response = @http_client.post(url, JSON.generate({ ott_id: ott_id, label_format: label_format }),
+                                       'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/taxonomy/taxon_info.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class Taxonomy
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module TaxonInfo
+        def taxon_info(**parameters)
+          ott_id = parameters[:ott_id]
+          source_id = parameters[:source_id]
+          validate_ott_and_source_id(ott_id, source_id)
+
+          url = 'https://api.opentreeoflife.org/v3/taxonomy/taxon_info'
+          response = @http_client.post(url, JSON.generate(parameters), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+
+        private
+
+        def validate_ott_and_source_id(ott_id, source_id)
+          raise ArgumentError, 'ott_id or source_id are required' if ott_id.nil? && source_id.nil?
+          raise ArgumentError, 'ott_id and source_id specified. Only 1 can be used' if !ott_id.nil? && !source_id.nil?
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tnrs/autocomplete_name.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TNRS
+      # tnrs autocomplete_name api endpoint
+      module AutocompleteName
+        def autocomplete_name(**parameters)
+          name = parameters[:name]
+          raise ArgumentError if name.nil?
+
+          context_name = parameters[:context_name]
+          include_suppressed = parameters[:include_suppressed]
+
+          payload = { name: name, context_name: context_name, include_suppressed: include_suppressed }.compact
+          url = 'https://api.opentreeoflife.org/v3/tnrs/autocomplete_name'
+          response = @http_client.post(url, JSON.generate(payload), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tnrs/base.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+require_relative './match_names'
+require_relative './autocomplete_name'
+require_relative './contexts'
+require_relative './infer_context'
+
+module Taxa
+  module OpenTreeOfLife
+    # TNRS api endpoints
+    class TNRS
+      include MatchNames
+      include AutocompleteName
+      include Contexts
+      include InferContext
+
+      attr_reader :http_client
+
+      def initialize(http_client)
+        @http_client = http_client
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tnrs/contexts.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TNRS
+      # tnrs contexts api endpoint
+      module Contexts
+        def contexts
+          url = 'https://api.opentreeoflife.org/v3/tnrs/contexts'
+          response = @http_client.post(url, nil, 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tnrs/infer_context.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TNRS
+      # tnrs contexts api endpoint
+      module InferContext
+        def infer_context(**parameters)
+          names = parameters[:names]
+          raise ArgumentError if names.nil?
+
+          payload = { names: names }
+          url = 'https://api.opentreeoflife.org/v3/tnrs/infer_context'
+          response = @http_client.post(url, JSON.generate(payload), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tnrs/match_names.rb

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TNRS
+      # tnrs match_names api endpoint
+      module MatchNames
+        def match_names(**parameters)
+          names = parameters[:names]
+          raise ArgumentError if names.nil?
+
+          context_name = parameters[:context_name]
+          do_approximate_matching = parameters[:do_approximate_matching] || false
+          include_suppressed = parameters[:include_suppressed]
+
+          payload = {
+            names: names,
+            context_name: context_name,
+            do_approximate_matching: do_approximate_matching,
+            include_suppressed: include_suppressed
+          }
+          url = 'https://api.opentreeoflife.org/v3/tnrs/match_names'
+          response = @http_client.post(url, JSON.generate(payload), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tree_of_life/about.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TreeOfLife
+      # tree of life about api endpoint
+      module About
+        def about
+          response = @http_client.post('https://api.opentreeoflife.org/v3/tree_of_life/about')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tree_of_life/base.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+require_relative './about'
+require_relative './node_info'
+require_relative './mrca'
+require_relative './subtree'
+require_relative './induced_subtree'
+require_relative '../label_format_helper'
+
+module Taxa
+  module OpenTreeOfLife
+    # wraps the tree of life API from Open Tree of Life
+    class TreeOfLife
+      include About
+      include NodeInfo
+      include Mrca
+      include Subtree
+      include InducedSubtree
+      include LabelFormatHelper
+
+      SUBTREE_FORMATS = %w[newick arguson].freeze
+
+      attr_reader :http_client
+
+      def initialize(http_client)
+        @http_client = http_client
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tree_of_life/induced_subtree.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TreeOfLife
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module InducedSubtree
+        def induced_subtree(**parameters)
+          ott_ids = parameters[:ott_ids]
+          node_ids = parameters[:node_ids]
+
+          validate_ott_and_node_ids(ott_ids, node_ids)
+
+          label_format = get_label_format('newick', **parameters)
+
+          payload = { node_ids: node_ids, ott_ids: ott_ids, label_format: label_format }.compact
+          url = 'https://api.opentreeoflife.org/v3/tree_of_life/induced_subtree'
+          response = @http_client.post(url, JSON.generate(payload), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+
+        private
+
+        def validate_ott_and_node_ids(ott_ids, node_ids)
+          raise ArgumentError, 'ott_ids or node_ids are required' if ott_ids.nil? && node_ids.nil?
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tree_of_life/mrca.rb

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TreeOfLife
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module Mrca
+        def mrca(**parameters)
+          valid = parameters[:ott_ids] || parameters[:node_ids]
+          raise ArgumentError unless valid
+
+          url = 'https://api.opentreeoflife.org/v3/tree_of_life/mrca'
+          response = @http_client.post(url, JSON.generate(parameters), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tree_of_life/node_info.rb

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TreeOfLife
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module NodeInfo
+        def node_info(**parameters)
+          valid = parameters[:ott_id] || parameters[:node_id] || parameters[:node_ids]
+          raise ArgumentError unless valid
+
+          url = 'https://api.opentreeoflife.org/v3/tree_of_life/node_info'
+          response = @http_client.post(url, JSON.generate(parameters), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/tree_of_life/subtree.rb

@@ -0,0 +1,50 @@
+# frozen_string_literal: true
+
+require 'faraday'
+require 'json'
+
+module Taxa
+  module OpenTreeOfLife
+    class TreeOfLife
+      # wrapper around the node_info tree of life endpoint for Open Tree of Life
+      module Subtree
+        def subtree(**parameters)
+          ott_id = parameters[:ott_id]
+          node_id = parameters[:node_id]
+
+          validate_ott_and_node_id(ott_id, node_id)
+
+          format = parameters[:format] || 'newick'
+          validate_format(format)
+
+          label_format = get_label_format(format, **parameters)
+
+          height_limit = get_height_limit(format, **parameters)
+          payload = { node_id: node_id, ott_id: ott_id, format: format, label_format: label_format,
+                      height_limit: height_limit }.compact
+          url = 'https://api.opentreeoflife.org/v3/tree_of_life/subtree'
+          response = @http_client.post(url, JSON.generate(payload), 'Content-Type' => 'application/json')
+          JSON.parse(response.body)
+        end
+
+        private
+
+        def validate_ott_and_node_id(ott_id, node_id)
+          raise ArgumentError, 'ott_id or node_id are required' if ott_id.nil? && node_id.nil?
+          raise ArgumentError, 'ott_id and node_id specified. Only 1 can be specified' if !ott_id.nil? && !node_id.nil?
+        end
+
+        def validate_format(format)
+          return if SUBTREE_FORMATS.include?(format)
+
+          raise ArgumentError, "format be one of the following #{SUBTREE_FORMATS.join(', ')}"
+        end
+
+        def get_height_limit(format, **parameters)
+          height_limit = parameters[:height_limit]
+          (format == 'arguson' ? 3 : -1) if height_limit.nil?
+        end
+      end
+    end
+  end
+end

data/lib/taxa/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module Taxa
+  VERSION = '0.1.0'
+end

data/taxa.gemspec

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+require_relative 'lib/taxa/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'taxa'
+  spec.version       = Taxa::VERSION
+  spec.authors       = ['Shane Sherman']
+  spec.email         = ['shane.sherman@gmail.com']
+
+  spec.summary       = 'Wrapper around a bunch of taxonomy databases.'
+  spec.description   = 'Wrapper around a bunch of taxonomy databases.'
+  spec.homepage      = 'https://github.com/ssherman/taxa'
+  spec.license       = 'MIT'
+  spec.required_ruby_version = Gem::Requirement.new('>= 2.7')
+
+  spec.metadata['homepage_uri'] = spec.homepage
+  spec.metadata['source_code_uri'] = 'https://github.com/ssherman/taxa'
+  spec.metadata['changelog_uri'] = 'https://github.com/ssherman/taxa/master/CHANGELOG.md'
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files = Dir.chdir(File.expand_path(__dir__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  end
+  spec.bindir        = 'exe'
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib']
+  spec.add_development_dependency 'rubocop', '~> 1.6'
+  spec.add_dependency 'faraday', '~> 1.1'
+  spec.add_dependency 'json', '~> 1.8'
+end

metadata

@@ -0,0 +1,127 @@
+--- !ruby/object:Gem::Specification
+name: taxa
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Shane Sherman
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2020-12-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: faraday
+  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: json
+  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'
+description: Wrapper around a bunch of taxonomy databases.
+email:
+- shane.sherman@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rubocop.yml"
+- ".travis.yml"
+- CHANGELOG.md
+- CODE_OF_CONDUCT.md
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/taxa.rb
+- lib/taxa/open_tree_of_life/client.rb
+- lib/taxa/open_tree_of_life/label_format_helper.rb
+- lib/taxa/open_tree_of_life/studies/base.rb
+- lib/taxa/open_tree_of_life/studies/find_studies.rb
+- lib/taxa/open_tree_of_life/studies/find_trees.rb
+- lib/taxa/open_tree_of_life/studies/properties.rb
+- lib/taxa/open_tree_of_life/studies/study.rb
+- lib/taxa/open_tree_of_life/studies/tree.rb
+- lib/taxa/open_tree_of_life/taxonomy/about.rb
+- lib/taxa/open_tree_of_life/taxonomy/base.rb
+- lib/taxa/open_tree_of_life/taxonomy/mrca.rb
+- lib/taxa/open_tree_of_life/taxonomy/subtree.rb
+- lib/taxa/open_tree_of_life/taxonomy/taxon_info.rb
+- lib/taxa/open_tree_of_life/tnrs/autocomplete_name.rb
+- lib/taxa/open_tree_of_life/tnrs/base.rb
+- lib/taxa/open_tree_of_life/tnrs/contexts.rb
+- lib/taxa/open_tree_of_life/tnrs/infer_context.rb
+- lib/taxa/open_tree_of_life/tnrs/match_names.rb
+- lib/taxa/open_tree_of_life/tree_of_life/about.rb
+- lib/taxa/open_tree_of_life/tree_of_life/base.rb
+- lib/taxa/open_tree_of_life/tree_of_life/induced_subtree.rb
+- lib/taxa/open_tree_of_life/tree_of_life/mrca.rb
+- lib/taxa/open_tree_of_life/tree_of_life/node_info.rb
+- lib/taxa/open_tree_of_life/tree_of_life/subtree.rb
+- lib/taxa/version.rb
+- taxa.gemspec
+homepage: https://github.com/ssherman/taxa
+licenses:
+- MIT
+metadata:
+  homepage_uri: https://github.com/ssherman/taxa
+  source_code_uri: https://github.com/ssherman/taxa
+  changelog_uri: https://github.com/ssherman/taxa/master/CHANGELOG.md
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '2.7'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.4
+signing_key: 
+specification_version: 4
+summary: Wrapper around a bunch of taxonomy databases.
+test_files: []