bark 0.0.2

checksums.yaml

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+SHA1:
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+  data.tar.gz: d2e60f6436a709252da45057b6790164c09aa117
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data/.gitignore

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+*.gem
+*.rbc
+/.config
+/coverage/
+/InstalledFiles
+/pkg/
+/spec/reports/
+/test/tmp/
+/test/version_tmp/
+/tmp/
+
+## Specific to RubyMotion:
+.dat*
+.repl_history
+build/
+
+## Documentation cache and generated files:
+/.yardoc/
+/_yardoc/
+/doc/
+/rdoc/
+
+## Environment normalisation:
+/.bundle/
+/lib/bundler/man/
+
+# for a library or gem, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# Gemfile.lock
+# .ruby-version
+# .ruby-gemset
+
+# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
+.rvmrc
+
+*~
+*.swp
+.DS_Store
+
+.idea
+idea/
+.idea/
+

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.1.2

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in bark_stub.gemspec
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    bark (0.0.1)
+      hashie (~> 3.3)
+      json (~> 1.8)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    awesome_print (1.2.0)
+    byebug (3.4.0)
+      columnize (~> 0.8)
+      debugger-linecache (~> 1.2)
+      slop (~> 3.6)
+    columnize (0.8.9)
+    debugger-linecache (1.2.0)
+    diff-lcs (1.2.5)
+    hashie (3.3.1)
+    json (1.8.1)
+    rake (10.3.2)
+    rspec (3.1.0)
+      rspec-core (~> 3.1.0)
+      rspec-expectations (~> 3.1.0)
+      rspec-mocks (~> 3.1.0)
+    rspec-core (3.1.0)
+      rspec-support (~> 3.1.0)
+    rspec-expectations (3.1.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.1.0)
+    rspec-mocks (3.1.0)
+      rspec-support (~> 3.1.0)
+    rspec-support (3.1.0)
+    slop (3.6.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  awesome_print (~> 1.2)
+  bark!
+  bundler (~> 1.5)
+  byebug (~> 3.4)
+  rake (~> 10.3)
+  rspec (~> 3.1)

data/LICENSE.txt

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+Copyright (c) 2014 Matt Yoder
+
+BSD
+

data/README.md

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+bark
+====
+
+[![Continuous Integration Status][6]][7]
+[![Dependency Status][8]][9]
+[rubydoc][1]
+
+Bark is a Ruby Gem wrapper on the [Open Tree of Life API][3]. It was written over the course of the [OpenTree hackathon][2]  At present it seeks to provide a simple (level 1 in terms of hackathon speak) wrapper over all of the API calls available, returning a native json object for each response. It also acts as a sanity checker on the API calls themselves, running a suite of unit tests shared by related wrappers in [Python][5] and [R][4].
+
+## Installation
+
+Bark is written targetting Ruby 2.1.x.
+
+Add this line to your application's Gemfile:
+
+    gem 'bark'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install bark
+
+## Usage
+
+Bark is broken down into Request and Response objects.  These are additionally wrapped with a set of helper methods that map 1:1 with the [Open Tree URLs][3].  Binding method names [follow a convention][10] adopted by the related Python and R frameworks.
+
+In your script:
+
+```
+  require 'bark'  # => true
+```
+
+### Simple usage
+
+```ruby
+  Bark.tol_about  # => { big hash }
+```
+
+Pass parameters like so:
+
+```ruby
+  Bark.get_study(params: {:study_id => '2113'})   # => {big json response}
+```
+
+Parameter keys can be symbols or strings. Available methods [are listed here][10].
+
+### Request/Response style
+
+```ruby
+    request = Bark::Request::Studies.new(method: :get_study, params: {study_id: '2113'})  # => #<Bark::Request::Studies:0x0000010310d340 @method=:get_study, @params={:study_id=>"2113"}, @uri=#<URI::HTTP:0x0000010310c508 URL:http://devapi.opentreeoflife.org/v2/study/2113>> 
+```
+
+Pre-check the validity of the requst (NOTE: mapping/checking is in development)
+
+```ruby
+    request.valid? # => true 
+```
+
+Get a response:
+
+```ruby
+    response = Bark::Response.new(request: request)  # =>  #<Bark::Response:0x0000010334c138 @json={ ... big response ... }
+    response.json   # =>  { ... big response ... }
+``` 
+
+## Documentation
+
+Documentation is autogenerated at [RubyDoc.info][1]
+
+## Contributing
+
+1. Fork it ( http://github.com/SpeciesFileGroup/bark/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request
+
+## Licence
+
+Bark is open source, it is available under the BSD licence.
+
+[1]: http://rubydoc.info/github/SpeciesFileGroup/bark/frames
+[2]: https://github.com/OpenTreeOfLife/hackathon  
+[3]: https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs
+[4]: https://github.com/fmichonneau/rotl
+[5]: https://github.com/OpenTreeOfLife/opentree-interfaces
+[6]: https://secure.travis-ci.org/SpeciesFileGroup/bark.png?branch=master
+[7]: http://travis-ci.org/SpeciesFileGroup/bark?branch=master
+[8]: https://gemnasium.com/SpeciesFileGroup/bark.png?branch=master
+[9]: https://gemnasium.com/SpeciesFileGroup/bark?branch=master
+[10]: https://github.com/OpenTreeOfLife/opentree/wiki/Libraries-for-working-with-opentree-in-various-languages-%28service-bindings-and-wrappers,-etc.%29
+
+

data/Rakefile

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+begin
+require 'rspec/core/rake_task'
+require "bundler/gem_tasks"
+
+      RSpec::Core::RakeTask.new(:spec)
+
+        task :default => :spec
+rescue LoadError
+    # no rspec available
+end

data/bark.gemspec

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+# coding: utf-8
+# 
+# Notes for deploying
+# gem build bark.gemspec
+# gem install ./bark-0.0.1.gem
+# gem yank bark -v 0.0.1
+# gem push bark-0.0.1.gem
+
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'bark/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "bark"
+  spec.version       = Bark::VERSION
+  spec.authors       = ["Matt Yoder"]
+  spec.email         = ["diapriid@gmail.com"]
+  spec.summary       = %q{A Ruby wrapper on the Open Tree API.}
+  spec.description   = %q{A wrapper on the Open Tree API, developed during the open tree hackathon in September, 2014.}
+  spec.homepage      = "https://github.com/SpeciesFileGroup/bark"
+  spec.license       = "BSD"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+  
+  spec.required_ruby_version = '~> 2.1'
+
+  spec.add_runtime_dependency 'json', '~> 1.8'
+  spec.add_runtime_dependency 'hashie', '~> 3.3'
+
+  spec.add_development_dependency "bundler", "~> 1.5"
+  spec.add_development_dependency "rake", "~> 10.3"
+  spec.add_development_dependency "byebug", "~> 3.4"
+  spec.add_development_dependency "rspec", '~> 3.1'
+  spec.add_development_dependency "awesome_print", '~> 1.2'
+
+end

data/lib/bark.rb

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+# encoding: UTF-8
+
+recent_ruby = RUBY_VERSION >= '2.1.0'
+raise "IMPORTANT:  gem requires ruby >= 2.1.0" unless recent_ruby
+
+require "bark/version"
+
+require "json"
+require "net/http"
+
+require_relative 'bark/request'
+require_relative 'bark/request/studies'
+require_relative 'bark/request/tree_of_life'
+require_relative 'bark/request/graph_of_life'
+require_relative 'bark/request/tnrs'
+require_relative 'bark/request/taxonomy'
+
+require_relative 'bark/response'
+
+class Bark
+
+  def self.request_class(method)
+    method = method.to_s
+    return Bark::Request::TreeOfLife  if method =~ /^tol_/ 
+    return Bark::Request::Tnrs        if method =~ /^tnrs_/ 
+    return Bark::Request::GraphOfLife if method =~ /^gol_/ 
+    return Bark::Request::Taxonomy    if method =~ /^taxonomy_/ 
+    return Bark::Request::Studies     if method =~ /^studies_|^get_study/ 
+    return false
+  end
+
+  # TODO: this needs more stress testing
+  def self.method_missing(meth, *args, &block)
+    if klass = self.request_class(meth)
+      if args[0].nil?
+        params = {}
+      else
+        params = args[0][:params]
+      end
+      params = {} if params.nil?
+      request = klass.new(method: meth, params: params, &block)
+      Bark::Response.new(request: request).result
+    else
+      super
+    end
+  end
+
+   #def self.tol_about(params: {}) 
+   #end
+
+   #def self.tol_mrca(params: {}) 
+   #end
+
+   #def self.tol_subtree(params: {}) 
+   #end
+
+   #def self.tol_induced_tree(params: {}) 
+   #end
+
+   #def self.gol_about(params: {}) 
+   #end
+
+   #def self.gol_source_tree(params: {}) 
+   #end
+
+   #def self.gol_node_info(params: {}) 
+   #end
+
+   #def self.tnrs_match_names(params: {}) 
+   #end
+
+   #def self.tnrs_contexts(params: {}) 
+   #end
+
+   #def self.tnrs_infer_context(params: {}) 
+   #end
+
+   #def self.taxonomy_about(params: {}) 
+   #end
+
+   #def self.taxonomy_lica(params: {}) 
+   #end
+
+   #def self.taxonomy_subtree(params: {}) 
+   #end
+
+   #def self.taxonomy_taxon(params: {}) 
+   #end
+
+   #def self.studies_find_studies(params: {})
+   #end
+
+   #def self.studies_find_trees(params: {}) 
+   #end
+
+   #def self.studies_properties(params: {}) 
+   #end
+
+   #def self.get_study(params: {}) 
+   #end
+
+   #def self.get_study_tree(params: {}) 
+   #end
+
+end
+
+class Bark::Error < StandardError
+
+end

data/lib/bark/request.rb

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+class Bark
+  class Request
+
+    # Target API https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs
+
+    BASE_URL = 'http://devapi.opentreeoflife.org'
+    attr_accessor :params, :method 
+    attr_accessor :payload 
+    attr_reader :uri
+
+    # TODO: super this
+    def initialize(options = {})
+      opts = {
+        format: 'foo', # Bark::Request::FORMAT,
+        method: :getSyntheticTree,
+        params: { }
+      }.merge!(options)
+
+      assign_options(opts)
+      build_uri if valid?
+    end
+
+    def assign_options(opts)
+      @method = opts[:method]
+      @format = opts[:format]
+      @params = opts[:params]
+
+    end
+
+    def uri
+      build_uri
+      @uri
+    end
+
+    def response
+      build_uri
+      if valid?
+        Response.new(request: self)
+      else
+        false # raise?
+      end
+    end
+
+    def params_are_supported? 
+      return false if @method.nil?
+      return true if self.class::METHODS[@method] == []
+      @params.keys.map(&:to_sym) - self.class::METHODS[@method] == []
+    end
+
+    def has_required_params?
+      return false if @method.nil?
+      return true if self.class::METHODS_REQUIRED_PARAMS[@method].nil?
+      self.class::METHODS_REQUIRED_PARAMS[@method].select{|v| !@params.keys.include?(v)} == []
+    end
+
+    # Stub for subclasses
+    def valid?
+    end
+
+    # stub for uri
+    def uri
+      build_uri
+      @uri
+    end
+
+    def json_payload
+    end
+
+    private 
+
+    # Stub for subclasses 
+    def build_uri
+      false
+    end
+
+  end
+end