bananomia 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
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+  data.tar.gz: 31f8e82c05f848423df644b365a923af0faa4f03b38e19dcffeafe0d5b680232
+SHA512:
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+  data.tar.gz: 8a1709dfed31dd27c2b83aad10bdfcc20c5ccc5ccd3689902904e66d5f7ca829ee385bc13ef2627c414610a5e3ac11347300b61ca38489c168d59d3d914b8944

data/.github/workflows/main.yml

@@ -0,0 +1,19 @@
+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: 3.1.3
+        bundler-cache: true
+    - name: Run the default task
+      run: bundle exec rake
+      env:
+        USER: ${{ vars.USER }}
+        PASSWORD: ${{ secrets.PASSWORD }}

data/.gitignore

@@ -0,0 +1,9 @@
+.idea
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/CHANGELOG.md

@@ -0,0 +1,5 @@
+## [Unreleased]
+
+## [0.1.0] - 2022-01-20
+
+- Initial release

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 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 bananomia.gemspec
+gemspec
+
+gem "rake", "~> 13.0"
+
+gem "minitest", "~> 5.0"

data/Gemfile.lock

@@ -0,0 +1,53 @@
+PATH
+  remote: .
+  specs:
+    bananomia (0.1.0)
+      faraday (~> 2.2)
+      faraday-follow_redirects (>= 0.1, < 0.4)
+      multi_json (~> 1.15)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.8.1)
+      public_suffix (>= 2.0.2, < 6.0)
+    byebug (11.1.3)
+    crack (0.4.5)
+      rexml
+    faraday (2.7.10)
+      faraday-net_http (>= 2.0, < 3.1)
+      ruby2_keywords (>= 0.0.4)
+    faraday-follow_redirects (0.3.0)
+      faraday (>= 1, < 3)
+    faraday-net_http (3.0.2)
+    hashdiff (1.0.1)
+    minitest (5.15.0)
+    multi_json (1.15.0)
+    power_assert (2.0.1)
+    public_suffix (5.0.1)
+    rake (13.0.6)
+    rexml (3.2.5)
+    ruby2_keywords (0.0.5)
+    test-unit (3.5.3)
+      power_assert
+    vcr (6.0.0)
+    webmock (3.18.1)
+      addressable (>= 2.8.0)
+      crack (>= 0.3.2)
+      hashdiff (>= 0.4.0, < 2.0.0)
+
+PLATFORMS
+  x86_64-linux
+
+DEPENDENCIES
+  bananomia!
+  bundler (~> 2.1, >= 2.1.4)
+  byebug
+  minitest (~> 5.0)
+  rake (~> 13.0)
+  test-unit (~> 3.3, >= 3.3.6)
+  vcr (~> 6.0)
+  webmock (~> 3.18)
+
+BUNDLED WITH
+   2.3.24

data/LICENSE.txt

@@ -0,0 +1,13 @@
+Copyright © 2023 Species File Group. All rights reserved.
+
+Developed by: Species File Group 
+Illinois Natural History Survey
+https://github.com/SpeciesFileGroup/bananomia
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal with 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:
+
+    Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers.
+    Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution.
+    Neither the names of <Name of Development Group, Name of Institution>, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission.
+
+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 CONTRIBUTORS 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 WITH THE SOFTWARE.

data/README.md

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+# Bananomia
+
+This is a Ruby wrapper on the [Bionomia](https://bionomia.net) API. Code follow 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 'bananomia'
+```
+
+And then execute:
+
+    $ bundle install
+
+Or install it yourself as:
+
+    $ gem install bananomia
+
+## Usage
+
+
+---
+### Suggest Collector Names
+Get collector name suggestions with a limit of 5:
+```ruby
+Bananomia.suggest('Smith, Ja', limit: 5) #  => MultiJson object
+```
+Filter suggestions to only public profiles
+```ruby
+Bananomia.suggest('Smith, Ja', is_public: true) #  => MultiJson object
+```
+Filter suggestions to only people that have occurrences associated with them:
+```ruby
+Bananomia.suggest('Smith, Ja', has_occurrences: true) #  => MultiJson object
+```
+
+---
+### Search Collectors
+Search for a collector by name:
+```ruby
+Bananomia.search_people('Thomas McElrath') #  => MultiJson object
+```
+
+Filter the people search by taxonomic families_collected or taxonomic families_identified. If strict is set to true, then matches must include the taxonomic families.
+```ruby
+Bananomia.search_people('Thomas McElrath', families_collected: 'Monotomidae', strict: true) #  => MultiJson object
+```
+```ruby
+Bananomia.search_people('Thomas McElrath', families_identified: 'Monotomidae', strict: true) #  => MultiJson object
+```
+
+Filter the search by whether the person was living on the specimen collection/identification date. If strict is set to true, it requires that they were alive on the date.
+```ruby
+Bananomia.search_people('Smith', date: '1580-01-02', strict: true) #  => MultiJson object
+```
+
+Setting the callback parameter returns [JSON-P](https://en.wikipedia.org/wiki/JSONP) wrapped in the provided callback string.
+```ruby
+Bananomia.search_people('Smith', callback: 'myFunction') #  => JSON-P object
+```
+
+Use the page parameter for pagination of the search results:
+```ruby
+Bananomia.search_people('Smith', page: 2) #  => MultiJson object
+```
+
+---
+### Search Occurrences
+Search for occurrences by [GBIF](https://gbif.org) [datasetID](https://www.gbif.org/dataset/f86a681d-7db8-483b-819a-248def18b70a) and [occurrenceID](https://www.gbif.org/occurrence/1804069383):
+```ruby
+Bananomia.search_occurrences('f86a681d-7db8-483b-819a-248def18b70a', '7a1daa39-8d7c-d7c4-968f-799d58b3c7b0') #  => MultiJson object
+```
+Setting the callback parameter returns [JSON-P](https://en.wikipedia.org/wiki/JSONP) wrapped in the provided callback string.
+```ruby
+Bananomia.search_occurrences('f86a681d-7db8-483b-819a-248def18b70a', '7a1daa39-8d7c-d7c4-968f-799d58b3c7b0', callback: 'myFunction') #  => JSON-P object
+```
+
+---
+### Collectors
+Get a person's profile by their [ORCID](https://orcid.org/) or [WikiData](https://wikidata.org) identifiers:
+```ruby
+Bananomia.person('0000-0001-7618-5230') #  => JSON-LD object
+```
+---
+### Specimens
+Get a person's specimens by their [ORCID](https://orcid.org/) or [WikiData](https://wikidata.org) identifiers. Use the page parameter for pagination.
+```ruby
+Bananomia.person('0000-0001-7618-5230', specimens: true) #  => JSON-LD object
+```
+
+```ruby
+Bananomia.person('0000-0001-7618-5230', specimens: true, csv: true) #  => comma-separated values
+```
+---
+### Occurrences
+Get an occurrence with a [GBIF](https://www.gbif.org/occurrence/search) occurrenceID:
+```ruby
+Bananomia.occurrence('477976412') #  => JSON-LD object
+```
+---
+### Parsing human names
+**Note:** [Bionomia](https://bionomia.net) provides a RESTful API for the human name parsing [dwc_agent](https://rubygems.org/gems/dwc_agent) gem which uses the [namae](https://rubygems.org/gems/namae) gem, and you likely will get better performance using those gems directly if parsing a large number of human names.
+
+Parse authorships with names separated by `;` and each authorship set separated by `\r\n`:
+```ruby
+Bananomia.parse(names: 'Henry Robert Nicollon des Abbayes; Groom Q\r\nMrs. John Errol Chandos Aberdeen') #  => MultiJson object
+```
+
+---
+
+## 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 the created tag, 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/SpeciesFileGroup/bananomia. 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/bananomia/blob/main/CODE_OF_CONDUCT.md).
+
+## License
+
+The gem is available as open source under the terms of the [NCSA/Illinois](https://github.com/SpeciesFileGroup/bananomia/blob/main/LICENSE.txt) license. You can learn more about the NCSA license on [Wikipedia](https://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License) and compare it with other open source licenses at the [Open Source Initiative](https://opensource.org/license/uoi-ncsa-php/).
+
+## Code of Conduct
+
+Everyone interacting in the Bananomia project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/SpeciesFileGroup/bananomia/blob/main/CODE_OF_CONDUCT.md).

data/Rakefile

@@ -0,0 +1,14 @@
+# 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/bananomia.gemspec

@@ -0,0 +1,56 @@
+# frozen_string_literal: true
+
+require_relative "lib/bananomia/version"
+
+Gem::Specification.new do |s|
+  s.name          = "bananomia"
+  s.version       = Bananomia::VERSION
+  s.authors       = ["Geoff Ower, Matt Yoder"]
+  s.email         = ["gdower@illinois.edu"]
+
+  s.summary       = "Bionomia Client"
+  s.description   = "Bananomia is a low-level wrapper around the Bionomia API."
+  s.homepage      = "https://github.com/SpeciesFileGroup/bananomia"
+  s.license       = "NCSA"
+  s.required_ruby_version = ">= 2.4.0"
+
+ # s.metadata["allowed_push_host"] = "TODO: Set to 'https://mygemserver.com'"
+
+  s.metadata["homepage_uri"] = s.homepage
+  s.metadata["source_code_uri"] = "https://github.com/SpeciesFileGroup/bananomia"
+  s.metadata["changelog_uri"] = "https://github.com/SpeciesFileGroup/bananomia/releases/tag/v#{s.version}"
+
+  # 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.
+  s.files = Dir.chdir(File.expand_path(__dir__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{\A(?:test|s|features)/}) }
+  end
+  s.bindir        = "exe"
+  s.executables   = s.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
+  s.require_paths = ["lib"]
+
+  # Uncomment to register a new dependency of your gem
+  # s.add_dependency "example-gem", "~> 1.0"
+
+  s.add_development_dependency "bundler", "~> 2.1", ">= 2.1.4"
+  # s.add_development_dependency "codecov", "~> 0.5.0"
+  # s.add_development_dependency "json", "~> 2.3", ">= 2.3.1"
+  s.add_development_dependency "rake", "~> 13.0", ">= 13.0.1"
+  # s.add_development_dependency "standard", "~> 1.0"
+  # s.add_development_dependency "simplecov", "~> 0.21.2"
+  s.add_development_dependency "test-unit", "~> 3.3", ">= 3.3.6"
+  s.add_development_dependency "vcr", "~> 6.0"
+  s.add_development_dependency "webmock", "~> 3.18"
+
+  s.add_runtime_dependency "faraday", "~> 2.2"
+  s.add_runtime_dependency "faraday-follow_redirects", ">= 0.1", "< 0.4"
+  s.add_runtime_dependency "multi_json", "~> 1.15"
+
+  # TODO: comment out
+  s.add_development_dependency "byebug"
+
+  #  s.add_runtime_dependency "thor", "~> 1.0", ">= 1.0.1"
+
+  # For more information and examples about making a new gem, checkout our
+  # guide at: https://bundler.io/guides/creating_gem.html
+end

data/bin/console

@@ -0,0 +1,15 @@
+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require "bundler/setup"
+require "bananomia"
+
+# 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

@@ -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/bananomia/error.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+module Bananomia
+    # Custom error class for rescuing from all Bananomia errors
+    class Error < StandardError; end
+  
+    # Raised when Bionomia returns the HTTP status code 400
+    class BadRequest < Error; end
+  
+    # Raised when Bionomia returns the HTTP status code 404
+    class NotFound < Error; end
+  
+    # Raised when Bionomia returns the HTTP status code 500
+    class InternalServerError < Error; end
+  
+    # Raised when Bionomia returns the HTTP status code 502
+    class BadGateway < Error; end
+  
+    # Raised when Bionomia returns the HTTP status code 503
+    class ServiceUnavailable < Error; end
+  
+    # Raised when Bionomia returns the HTTP status code 504
+    class GatewayTimeout < Error; end
+  end

data/lib/bananomia/faraday.rb

@@ -0,0 +1,73 @@
+# frozen_string_literal: true
+
+require "faraday"
+require "multi_json"
+
+# @private
+module Faraday
+  module ColrapiErrors
+    # @private
+    class Middleware < Faraday::Middleware
+      def call(env)
+        @app.call(env).on_complete do |response|
+          case response[:status].to_i
+          when 400
+            raise Bananomia::BadRequest, error_message_400(response)
+          when 404
+            raise Bananomia::NotFound, error_message_400(response)
+          when 500
+            raise Bananomia::InternalServerError, error_message_500(response, "Something is technically wrong.")
+          when 502
+            raise Bananomia::BadGateway, error_message_500(response, "The server returned an invalid or incomplete response.")
+          when 503
+            raise Bananomia::ServiceUnavailable, error_message_500(response, "Crossref is rate limiting your requests.")
+          when 504
+            raise Bananomia::GatewayTimeout, error_message_500(response, "504 Gateway Time-out")
+          end
+        end
+      end
+
+      def initialize(app)
+        super app
+        @parser = nil
+      end
+
+      private
+
+      def error_message_400(response)
+        "\n   #{response[:method].to_s.upcase} #{response[:url]}\n   Status #{response[:status]}#{error_body(response[:body])}"
+      end
+
+      def error_body(body)
+        if !body.nil? && !body.empty? && body.is_a?(String)
+          if json?(body)
+            body = ::MultiJson.load(body)
+            if body["message"].nil?
+              body = nil
+            else
+              body = body["message"]
+            end
+          end
+        end
+
+        if body.nil?
+          nil
+        else
+          ": #{body}"
+        end
+      end
+
+      def error_message_500(response, body = nil)
+        "#{response[:method].to_s.upcase} #{response[:url]}: #{[response[:status].to_s + ":", body].compact.join(" ")}"
+      end
+
+      def json?(string)
+        MultiJson.load(string)
+        true
+      rescue MultiJson::ParseError
+        false
+      end
+    end
+  end
+end
+

data/lib/bananomia/helpers/configuration.rb

@@ -0,0 +1,26 @@
+# 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/bananomia/request.rb

@@ -0,0 +1,82 @@
+require_relative "faraday" # !! Potential ruby 3.0 difference in module loading? relative differs from Serrano
+require "faraday/follow_redirects"
+require_relative "utils"
+
+module Bananomia
+
+  class Request
+    attr_accessor :endpoint
+    attr_accessor :q
+    attr_accessor :verbose
+
+    attr_accessor :options
+
+    def initialize(**args)
+      @endpoint = args[:endpoint]
+      @verbose = args[:verbose]
+      @q = args[:q]
+      @families_collected = args[:families_collected]
+      @families_identified = args[:families_identified]
+      @date = args[:date]
+      @strict = args[:strict]
+      @callback = args[:callback]
+      @is_public = args[:is_public]
+      @has_occurrences = args[:has_occurrences]
+      @dataset_id = args[:dataset_id]
+      @occurrence_id = args[:occurrence_id]
+      @names = args[:names]&.gsub('\n', "\n")&.gsub('\r', "\r")
+      @limit = args[:limit]
+      @page = args[:page]
+      @options = args[:options] # TODO: not added at bananomia.rb
+    end
+
+    def perform
+
+      args = {
+        q: @q,
+        families_collected: @families_collected,
+        families_identified: @families_identified,
+        date: @date,
+        strict: @strict,
+        callback: @callback,
+        names: @names,
+        is_public: @is_public,
+        has_occurrences: @has_occurrences,
+        datasetKey: @dataset_id,
+        occurrenceID: @occurrence_id,
+        limit: @limit,
+        page: @page
+      }
+      opts = args.delete_if { |_k, v| v.nil? }
+
+      Faraday::Utils.default_space_encoding = "+"
+
+      conn = if verbose
+               Faraday.new(url: Bananomia.base_url) do |f|
+                 f.response :logger
+                 f.use Faraday::ColrapiErrors::Middleware
+                 f.adapter Faraday.default_adapter
+               end
+             else
+               Faraday.new(url: Bananomia.base_url) do |f|
+                 f.use Faraday::ColrapiErrors::Middleware
+                 f.adapter Faraday.default_adapter
+               end
+             end
+
+      conn.headers['Accept'] = 'application/ld+json,*/*'
+      conn.headers[:user_agent] = make_user_agent
+      conn.headers["X-USER-AGENT"] = make_user_agent
+
+      res = conn.get(endpoint, opts)
+
+      # Handles ChecklistBank endpoints that do not return JSON
+      begin
+        MultiJson.load(res.body)
+      rescue MultiJson::ParseError
+        res.body
+      end
+      
+    end
+  end
+end

data/lib/bananomia/utils.rb

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+# From https://raw.githubusercontent.com/sckott/serrano/main/lib/serrano/utils.rb
+
+def make_user_agent
+  requa = "Faraday/v" + Faraday::VERSION
+  habua = "Bananomia/v" + Bananomia::VERSION
+  ua = requa + " " + habua
+  if Bananomia.mailto
+    ua += " (mailto:%s)" % Bananomia.mailto
+  end
+  # ua += format(' (mailto:%s)', Bananomia.mailto) if Bananomia.mailto
+  ua
+end
+
+def field_query_handler(x)
+  tmp = x.keep_if { |z| z.match(/query_/) }
+  rename_query_filters(tmp)
+end
+
+def rename_query_filters(foo)
+  foo = foo.tostrings
+  foo = foo.map { |x, y| [x.to_s.sub("container_title", "container-title"), y] }.to_h
+  foo.map { |x, y| [x.to_s.sub("query_", "query."), y] }.to_h
+end
+
+class Hash
+  def tostrings
+    map { |(k, v)| [k.to_s, v] }.to_h
+  end
+end
+
+class Hash
+  def tosymbols
+    map { |(k, v)| [k.to_sym, v] }.to_h
+  end
+end
+

data/lib/bananomia/version.rb

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

data/lib/bananomia.rb

@@ -0,0 +1,137 @@
+# frozen_string_literal: true
+
+require "erb"
+require_relative "bananomia/error"
+require_relative "bananomia/version"
+require_relative "bananomia/request"
+require "bananomia/helpers/configuration"
+
+module Bananomia
+  extend Configuration
+
+  define_setting :base_url, "https://api.bionomia.net/"
+  define_setting :mailto, ENV["BIONOMIA_API_EMAIL"]
+
+  # Parse human names
+  #
+  # @param names [String] Human name(s) separated by \r\n
+  #
+  # @param verbose [Boolean] Print headers to STDOUT
+  #
+  # @return [Array, Boolean] An array of hashes
+  def self.parse(names, verbose: false)
+    endpoint = "parse"
+    Request.new(
+      endpoint: endpoint,
+      names: names,
+      verbose: verbose
+    ).perform
+  end
+
+  # Get a person's profile by ID or specimens
+  # @param id [String] An ORCID or WikiData identifier
+  # @param specimens [Boolean, nil] Get the person's specimens
+  # @param csv [Boolean, nil] For specimens, whether to return a csv
+  #
+  # @param page [Integer, nil] Pagination for the results list
+  # @param verbose [Boolean] Print headers to STDOUT
+  #
+  # @return [Hash, String, Boolean] A JSON-LD hash or CSV
+  def self.person(id, csv: nil, specimens: nil, page: nil, verbose: false)
+    if csv and specimens
+      extension = '.csv'
+    else
+      extension = '.jsonld'
+    end
+
+    if specimens
+      endpoint = "#{id}/specimens#{extension}"
+    else
+      endpoint = "#{id}#{extension}"
+    end
+    Request.new(endpoint: endpoint, page: page, verbose: verbose).perform
+  end
+
+  # Get and occurrence record
+  # @param id [String] An occurence ID from Global Biodiversity Information Facility
+  #
+  # @param verbose [Boolean] Print headers to STDOUT
+  #
+  # @return [Hash, Boolean] A JSON-LD hash
+  def self.occurrence(id, verbose: false)
+    endpoint = "occurrence/#{id}.jsonld"
+    Request.new(endpoint: endpoint, verbose: verbose).perform
+  end
+
+  # Search human names
+  # @param q [String] A single human name
+  # @param families_collected [Boolean, nil] Comma-separated list of taxonomic families collected
+  # @param families_identified [Boolean, nil] Comma-separated list of taxonomic families identified
+  # @param date [String, nil] Filters to alive during date (format: YYYY-MM-DD, YYYY-MM, or YYYY)
+  #   e.g., Captain John Smith was alive from 1580-01-01 through 1631-06-21, so setting date to any value between
+  #         their birth/death date will include Captain John in the search results
+  #   Warning: Setting exactly equal to a person's birthdate, excludes them from search!
+  # @param strict [Boolean, nil] Must include vs should include on families_identified, families_collected, date
+  # @param callback [String, nil] A string to produce a JSONP response instead of a JSON-LD response
+  #
+  # @param page [Integer, nil] Pagination for the results list
+  # @param verbose [Boolean] Print headers to STDOUT
+  #
+  # @return [Array, Boolean] An array of hashes
+  def self.search_people(q, families_collected: nil, families_identified: nil, date: nil, page: nil,
+                  strict: nil, callback: nil, verbose: false)
+    endpoint = 'users/search'
+    Request.new(
+      endpoint: endpoint,
+      q: q,
+      families_collected: families_collected,
+      families_identified: families_identified,
+      date: date,
+      page: page,
+      strict: strict,
+      callback: callback,
+      verbose: verbose
+    ).perform
+  end
+
+  # Search occurrences
+  # @param dataset_id [String] a registered dataset UUID provided by the Global Biodiversity Information Facility
+  # @param occurrence_id [String] identifier from the data provider
+  # @param callback [String, nil] A string to produce a JSONP response instead of a JSON-LD response
+  #
+  # @param page [Integer, nil] Pagination for the results list
+  # @param verbose [Boolean] Print headers to STDOUT
+  #
+  # @return [Array, Boolean] An array of hashes
+  def self.search_occurrences(dataset_id, occurrence_id, callback: nil, verbose: false)
+    endpoint = 'occurrences/search'
+    Request.new(
+      endpoint: endpoint,
+      dataset_id: dataset_id,
+      occurrence_id: occurrence_id,
+      callback: callback,
+      verbose: verbose
+    ).perform
+  end
+
+  # Suggest human names (autocomplete widget)
+  # @param q [String] Part of a human name
+  # @param is_public [Boolean, nil] Filters results to public profiles
+  # @param has_occurrences [Boolean, nil] Filters results to profiles with occurrences
+  #
+  # @param limit [Integer, nil] The number of results to return
+  # @param verbose [Boolean] Print headers to STDOUT
+  #
+  # @return [Array, Boolean] An array of hashes
+  def self.suggest(q, is_public: nil, has_occurrences: nil, limit: nil, verbose: false)
+    endpoint = 'user.json'
+    Request.new(
+      endpoint: endpoint,
+      q: q,
+      is_public: is_public,
+      has_occurrences: has_occurrences,
+      limit: limit,
+      verbose: verbose
+    ).perform
+  end
+end

metadata

@@ -0,0 +1,215 @@
+--- !ruby/object:Gem::Specification
+name: bananomia
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Geoff Ower, Matt Yoder
+autorequire:
+bindir: exe
+cert_chain: []
+date: 2023-08-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.1.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.1.4
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 13.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 13.0.1
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.3.6
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.3.6
+- !ruby/object:Gem::Dependency
+  name: vcr
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '6.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '6.0'
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.18'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.18'
+- !ruby/object:Gem::Dependency
+  name: faraday
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.2'
+- !ruby/object:Gem::Dependency
+  name: faraday-follow_redirects
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0.1'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0.1'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+- !ruby/object:Gem::Dependency
+  name: multi_json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Bananomia is a low-level wrapper around the Bionomia API.
+email:
+- gdower@illinois.edu
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".github/workflows/main.yml"
+- ".gitignore"
+- CHANGELOG.md
+- CODE_OF_CONDUCT.md
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- bananomia.gemspec
+- bin/console
+- bin/setup
+- lib/bananomia.rb
+- lib/bananomia/error.rb
+- lib/bananomia/faraday.rb
+- lib/bananomia/helpers/configuration.rb
+- lib/bananomia/request.rb
+- lib/bananomia/utils.rb
+- lib/bananomia/version.rb
+homepage: https://github.com/SpeciesFileGroup/bananomia
+licenses:
+- NCSA
+metadata:
+  homepage_uri: https://github.com/SpeciesFileGroup/bananomia
+  source_code_uri: https://github.com/SpeciesFileGroup/bananomia
+  changelog_uri: https://github.com/SpeciesFileGroup/bananomia/releases/tag/v0.1.0
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.4.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.4.10
+signing_key:
+specification_version: 4
+summary: Bionomia Client
+test_files: []