taxa 0.1.0 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: bc7d986ed381cdb8284eec26e8f84e85d0ef803c00faf6b4f89cd178524b099c
-  data.tar.gz: e6edb9b337a03a9cb3ecfb16b81022044029dcb753009fe9526dcae10e5ff21a
+  metadata.gz: 0c3d0340e64965b829135fd758847296d007e8293d5229fd2485fccb40abe0be
+  data.tar.gz: 9c053380d21709436c7bf9b4e0a9198eecdedab7e0e578b4c50b992dcb4bd76e
 SHA512:
-  metadata.gz: c93fe05a6e816d72009f9c8178edb6d7a012fadcf309bdfee2cb37f886a1a0142a1245415eb620fadab6d057c55d3b342c5eddc0ce2e27763cac9ebfce9077fd
-  data.tar.gz: bf4b4afe570f496caf9b537b198223eb52a3fbc4e7cca4e36723bd019f817879f6ad0e877d647d63eff95f4dcb78acbd9b3222229b3b7e38210696efad95dcb2
+  metadata.gz: 99741a996cd69e5d57b2da6af6d0c4acf04a429db6258f6cdefbeb21d3b062aeba41a6537e7f5a3c6ff78d5941c533448b7263751ec134029bb9bad2538a29a3
+  data.tar.gz: 01d2cee9562d2f2845fc0866c3a8a68a279e548b5eb6f1913b41aa43110e8a13cc379b980e5ce524dc8165d5b18e7d003bd74cc09ad09425a5f466fdae8e3230

data/.ruby-version

@@ -0,0 +1 @@
+2.7.2

data/CHANGELOG.md

@@ -1 +1,29 @@
-nothing yet
+# Taxa Changelog
+
+## [0.1.0]
+
+### Highlights
+Support for Open Tree of Life API v3
+https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs
+
+## [0.2.0]
+
+### Highlights
+Support for the classic API for EOL
+https://eol.org/docs/what-is-eol/classic-apis
+
+## [0.2.1]
+
+### Highlights
+Update JSON gem to 2.5.x
+
+## [0.3.0]
+
+### Highlights
+Support for Plants of the World Online
+http://plantsoftheworldonline.org/
+
+## [0.3.1]
+
+### Highlights
+Fixed a bug related to Plants of The World Online filter validation

data/Gemfile.lock

@@ -1,18 +1,20 @@
 PATH
   remote: .
   specs:
-    taxa (0.1.0)
+    taxa (0.3.0)
       faraday (~> 1.1)
-      json (~> 1.8)
+      json (~> 2.5)
 
 GEM
   remote: https://rubygems.org/
   specs:
     ast (2.4.1)
-    faraday (1.1.0)
+    faraday (1.3.0)
+      faraday-net_http (~> 1.0)
       multipart-post (>= 1.2, < 3)
       ruby2_keywords
-    json (1.8.6)
+    faraday-net_http (1.0.1)
+    json (2.5.1)
     minitest (5.14.2)
     multipart-post (2.1.1)
     parallel (1.20.1)
@@ -34,7 +36,7 @@ GEM
     rubocop-ast (1.3.0)
       parser (>= 2.7.1.5)
     ruby-progressbar (1.10.1)
-    ruby2_keywords (0.0.2)
+    ruby2_keywords (0.0.4)
     unicode-display_width (1.7.0)
 
 PLATFORMS
@@ -47,4 +49,4 @@ DEPENDENCIES
   taxa!
 
 BUNDLED WITH
-   2.1.4
+   2.2.3

data/README.md

@@ -1,6 +1,6 @@
 # Taxa
 
-Taxa allows users to search multiple taxonomic data sources. Currently only Open Tree of Life is implemented.
+Taxa allows users to search multiple taxonomic data sources. Currently only Open Tree of Life and EOL classic APIs are implemented.
 
 ## Installation
 
@@ -19,8 +19,21 @@ Or install it yourself as:
     $ gem install taxa
 
 ## Usage
+```ruby
+tol_client = Taxa::OpenTreeOfLife::Client.new
+tol_client.tnrs.match_names('Cotyledon') # can be an array or a string
+
+eol_client = Taxa::EOLClassic::Client.new
+eol_client.hierarchy_entries(7834469)
+
+powo_client = Taxa::PlantsOfTheWorldOnline::Client.new
+powo_client.search('Crassula alata')
+powo_client.search('Crassula', ['species_f', 'has_images'])
+powo_client.search('family:Crassulaceae', ['species_f', 'has_images'])
+```
 
-client = Taxa::OpenTreeOfLife::Client.new
+For Plants of the World Online please see their official python library for available search terms: 
+https://github.com/RBGKew/pykew#available-search-terms-1
 
 ## Development
 

data/lib/taxa.rb

@@ -1,7 +1,10 @@
 # frozen_string_literal: true
 
 require 'taxa/version'
+require 'faraday'
 require_relative './taxa/open_tree_of_life/client'
+require_relative './taxa/eol_classic/client'
+require_relative './taxa/plants_of_the_world_online/client'
 
 module Taxa
   # include OpenTreeOfLife

data/lib/taxa/eol_classic/client.rb

@@ -0,0 +1,65 @@
+# frozen_string_literal: true
+
+module Taxa
+  module EOLClassic
+    # API client for Open Tree of Life
+    class Client
+      attr_accessor :options
+      attr_reader :http_client
+
+      def initialize(**options)
+        @options = options
+
+        @http_client = options[:http_client] || Faraday.new
+      end
+
+      def search(query, **parameters)
+        raise ArgumentError, 'query can not be nil' if query.nil?
+
+        url = 'https://eol.org/api/search/1.0.json'
+        response = @http_client.get(url, { q: query }.merge(parameters), { 'Accept' => 'application/json' })
+        parse_response(response)
+      end
+
+      def collections(id, **parameters)
+        raise ArgumentError, 'id can not be nil' if id.nil?
+
+        url = "https://eol.org/api/collections/1.0/#{id}.json"
+        response = @http_client.get(url, parameters, { 'Accept' => 'application/json' })
+        parse_response(response)
+      end
+
+      def pages(id, **parameters)
+        raise ArgumentError, 'id can not be nil' if id.nil?
+
+        url = "https://eol.org/api/pages/1.0/#{id}.json"
+        response = @http_client.get(url, parameters, { 'Accept' => 'application/json' })
+        parse_response(response)
+      end
+
+      def data_objects(id, **parameters)
+        raise ArgumentError, 'id can not be nil' if id.nil?
+
+        url = "https://eol.org/api/data_objects/1.0/#{id}.json"
+        response = @http_client.get(url, parameters, { 'Accept' => 'application/json' })
+        parse_response(response)
+      end
+
+      def hierarchy_entries(id, **parameters)
+        raise ArgumentError, 'id can not be nil' if id.nil?
+
+        url = "https://eol.org/api/hierarchy_entries/1.0/#{id}.json"
+        response = @http_client.get(url, parameters, { 'Accept' => 'application/json' })
+        parse_response(response)
+      end
+
+      private
+
+      def parse_response(response)
+        JSON.parse(response.body)
+      rescue StandardError
+        nil
+      end
+    end
+  end
+end

data/lib/taxa/open_tree_of_life/client.rb

@@ -4,7 +4,6 @@ require_relative './tnrs/base'
 require_relative './tree_of_life/base'
 require_relative './taxonomy/base'
 require_relative './studies/base'
-require 'faraday'
 
 module Taxa
   module OpenTreeOfLife

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa
@@ -10,10 +9,10 @@ module Taxa
       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')
+          response = @http_client.post(url, JSON.generate({ ott_ids: Array(ott_ids) }),
+                                       'Content-Type' => 'application/json')
           JSON.parse(response.body)
         end
       end

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa
@@ -8,20 +7,20 @@ module Taxa
     class TNRS
       # tnrs match_names api endpoint
       module MatchNames
-        def match_names(**parameters)
-          names = parameters[:names]
-          raise ArgumentError if names.nil?
+        def match_names(names, **parameters)
+          raise ArgumentError, 'names is required' if names.nil?
 
           context_name = parameters[:context_name]
           do_approximate_matching = parameters[:do_approximate_matching] || false
           include_suppressed = parameters[:include_suppressed]
 
           payload = {
-            names: names,
+            names: Array(names),
             context_name: context_name,
             do_approximate_matching: do_approximate_matching,
             include_suppressed: include_suppressed
-          }
+          }.compact
+
           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)

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

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

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-require 'faraday'
 require 'json'
 
 module Taxa

data/lib/taxa/plants_of_the_world_online/client.rb

@@ -0,0 +1,63 @@
+# frozen_string_literal: true
+
+require_relative '../utils'
+module Taxa
+  module PlantsOfTheWorldOnline
+    # API client for Open Tree of Life
+    class Client
+      attr_accessor :options
+      attr_reader :http_client
+
+      POWO_URL = 'http://www.plantsoftheworldonline.org/api/2'
+
+      FILTERS = %w[accepted_names has_images families_f genus_f species_f infraspecific_f].freeze
+
+      def initialize(**options)
+        @options = options
+        @http_client = options[:http_client] || Faraday.new
+      end
+
+      def search(query, options = {})
+        options.transform_keys!(&:to_sym)
+
+        page = options[:page] || 0
+        filters = Array.wrap(options[:filters])
+        validate_search_parameters(query, page, filters)
+
+        payload = { q: query, p: page }
+        payload.merge!({ f: filters.join(',') }) unless filters.empty?
+        response = @http_client.get("#{POWO_URL}/search", payload, { 'Accept' => 'application/json' })
+        parse_response(response)
+      end
+
+      def lookup(id, include = nil)
+        raise ArgumentError, 'id can not be nil' if id.nil?
+
+        include = Array.wrap(include)
+        payload = {}
+        payload.merge!({ fields: include.join(',') }) unless include.empty?
+        response = @http_client.get("#{POWO_URL}/taxon/#{id}", payload, { 'Accept' => 'application/json' })
+        parse_response(response)
+      end
+
+      private
+
+      def validate_search_parameters(query, page, filters)
+        raise ArgumentError, 'query can not be nil' if query.nil?
+
+        if !filters.empty? && !filters.all? { |f| FILTERS.include? f }
+          raise ArgumentError,
+                "filter is invalid. It must be one of these: #{FILTERS.join(', ')} can not be nil"
+        end
+
+        raise ArgumentError, 'page must be an integer' unless page.is_a?(Integer)
+      end
+
+      def parse_response(response)
+        JSON.parse(response.body)
+      rescue StandardError
+        nil
+      end
+    end
+  end
+end

data/lib/taxa/utils.rb

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+# https://stackoverflow.com/questions/18358717/ruby-elegantly-convert-variable-to-an-array-if-not-an-array-already
+class Array
+  def self.wrap(object)
+    if object.nil?
+      []
+    elsif object.respond_to?(:to_ary)
+      object.to_ary || [object]
+    else
+      [object]
+    end
+  end
+end

data/lib/taxa/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Taxa
-  VERSION = '0.1.0'
+  VERSION = '0.3.1'
 end

data/taxa.gemspec

@@ -28,5 +28,5 @@ Gem::Specification.new do |spec|
   spec.require_paths = ['lib']
   spec.add_development_dependency 'rubocop', '~> 1.6'
   spec.add_dependency 'faraday', '~> 1.1'
-  spec.add_dependency 'json', '~> 1.8'
+  spec.add_dependency 'json', '~> 2.5'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: taxa
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.3.1
 platform: ruby
 authors:
 - Shane Sherman
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2020-12-27 00:00:00.000000000 Z
+date: 2021-03-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubocop
@@ -44,14 +44,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '2.5'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '2.5'
 description: Wrapper around a bunch of taxonomy databases.
 email:
 - shane.sherman@gmail.com
@@ -61,6 +61,7 @@ extra_rdoc_files: []
 files:
 - ".gitignore"
 - ".rubocop.yml"
+- ".ruby-version"
 - ".travis.yml"
 - CHANGELOG.md
 - CODE_OF_CONDUCT.md
@@ -72,6 +73,7 @@ files:
 - bin/console
 - bin/setup
 - lib/taxa.rb
+- lib/taxa/eol_classic/client.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
@@ -96,6 +98,8 @@ files:
 - 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/plants_of_the_world_online/client.rb
+- lib/taxa/utils.rb
 - lib/taxa/version.rb
 - taxa.gemspec
 homepage: https://github.com/ssherman/taxa