taxa 0.1.1 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9326adca4c92b4369f90c78c0407bd7d2b03d01ed090dfa7de9316f433b9c075
-  data.tar.gz: 7d9e7ae022d84889381b95bd8176287789cef60144100d8e507f224483919675
+  metadata.gz: f193e48919a8c656ca30f3d15684f312d2366f429cf9aa2fefc6898799209cdc
+  data.tar.gz: c18067f427688d65538158f3649bfad96e180f211b7d85d84370db14827bc43c
 SHA512:
-  metadata.gz: f4245d41126fbb024c57eddcb53696b4e143725980c0aa08de6b3d8068ef2bd8d393e6835c5494055c40a652c21001a419af145cabc2a2f9b36601988aa098ac
-  data.tar.gz: 7276d724cfb346763a9c5a2db940fa75cd1e49a221c506f8bda2f1560f2ba3a34390e047000fd564978a01f44a1ac8a6e3ed3a05544d9aebb2a8e76a352e6bdc
+  metadata.gz: 9d4617f0daab6dcbeed3f06491f9430c1da29b9ceb3aae4cd31f0e80880d77aa8e7e899811d08baaf15f87f14fd63aa9d5daa14a63dbdd76ba190a8bc58aa414
+  data.tar.gz: bfb6575de0de6958a86c46d0096de0fb3149c08387ea5836e68b86f94c3556ab50fada6acd91aae5c0631814985a3a6c26a23f83d10ef4892274cbf8217dd98c

data/CHANGELOG.md

@@ -1 +1,13 @@
-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

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    taxa (0.1.0)
+    taxa (0.2.0)
       faraday (~> 1.1)
       json (~> 1.8)
 
@@ -9,9 +9,11 @@ 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
+    faraday-net_http (1.0.0)
     json (1.8.6)
     minitest (5.14.2)
     multipart-post (2.1.1)

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 +19,13 @@ 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
 
-client = Taxa::OpenTreeOfLife::Client.new
+eol_client = Taxa::EOLClassic::Client.new
+eol_client.hierarchy_entries(7834469)
+```
 
 ## Development
 

data/lib/taxa.rb

@@ -1,7 +1,9 @@
 # frozen_string_literal: true
 
 require 'taxa/version'
+require 'faraday'
 require_relative './taxa/open_tree_of_life/client'
+require_relative './taxa/eol_classic/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
@@ -12,7 +11,8 @@ module Taxa
           raise ArgumentError, 'ott_ids required' if ott_ids.nil?
 
           url = 'https://api.opentreeoflife.org/v3/taxonomy/mrca'
-          response = @http_client.post(url, JSON.generate({ ott_ids: Array(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

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/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Taxa
-  VERSION = '0.1.1'
+  VERSION = '0.2.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: taxa
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.2.0
 platform: ruby
 authors:
 - Shane Sherman
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2020-12-28 00:00:00.000000000 Z
+date: 2021-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubocop
@@ -72,6 +72,7 @@ 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