idigbio_client 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: c93a98a42c4cd9936bbca8f3b37dfbbf052590a0
+  data.tar.gz: ef51fb9364dc76e6734ed92d9e21808cdf895272
+SHA512:
+  metadata.gz: 9118912a42a83674c8e7bcbbd378a5830e6955df18da2098d688cebd4fd5b668b18bb61b3b7d4d36d8bbfbf2199d61c7ea6ebd607511d1de655f34b0c0048df4
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data/.gitignore

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

data/.rspec

@@ -0,0 +1,3 @@
+--format documentation
+--color
+--require spec_helper

data/.rubocop.yml

@@ -0,0 +1,12 @@
+AllCops:
+  Exclude:
+    - db/**/*
+    - bundle_bin/**/*
+  Include:
+    - exe/idigbio
+Metrics/ModuleLength:
+  Max: 1000
+Style/StringLiterals:
+  EnforcedStyle: double_quotes
+Style/DotPosition:
+  EnforcedStyle: trailing

data/.travis.yml

@@ -0,0 +1,11 @@
+language: ruby
+rvm:
+  - 1.9
+  - 2.0
+  - 2.1
+  - 2.2
+script:
+  - bundle exec rake
+branches:
+  only:
+      - master

data/CHANGELOG.md

@@ -0,0 +1,8 @@
+gn_crossmap CHANGELOG
+=====================
+
+0.1.0
+-----
+- [Dmitry Mozzherin][dimus] - initial version
+
+[dimus]: https://github.com/dimus

data/Gemfile

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

data/LICENSE

@@ -0,0 +1,20 @@
+Copyright (c) 2015 Marine Biological Laboratory
+
+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

@@ -0,0 +1,188 @@
+IdigbioClient
+=============
+
+[![Gem Version][gem_badge]][gem_link]
+[![Continuous Integration Status][ci_badge]][ci_link]
+[![Coverage Status][cov_badge]][cov_link]
+[![CodeClimate][code_badge]][code_link]
+[![Dependency Status][dep_badge]][dep_link]
+
+
+`idigbio_client` is a Ruby wrapper for [iDigBio API][api]
+
+
+Installation
+------------
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'idigbio_client'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install idigbio_client
+
+Usage
+-----
+
+Client functions can be grouped in 4 catetories
+
+* [inspect][inspect] - introspective methods
+* [search][search] - search by provided parameters
+* [show][show] - show any one object based on its UUID
+* [stats][stats] - various statistical data
+
+### Inspect
+
+Methos in this section supply metainformation important for effective use
+of the client.
+
+#### Method `IdigbioClient.types`
+
+Returns an array of types (resources) available via API.
+
+```ruby
+require "idigbio_client"
+
+IdigbioClient.types
+```
+
+#### Method `IdigbioClient.fields(type)
+
+Returns a hash with description of fields associated with a resource. Takes one
+optional parameter `type`. If type is not given it returns fields to all types
+in a hash.
+
+| Parameter  | Type             | Description                                                   |
+|------------|------------------|---------------------------------------------------------------|
+| type       | String or Symbol | indicates which type to query for its fields; *default* `nil` |
+
+```ruby
+require "idigbio_client"
+
+IdigbioClient.fields
+
+# fields of a specific type
+IdigbioClient.fields(:mediarecords)
+IdigbioClient.fields("records")
+```
+
+### Search
+
+#### Method `IdigbioClient.search(opts)`
+
+Takes a hash of opts, returns a hash with results of a search.
+
+| opts.keys  | Type             | Description                            |
+|------------|------------------|----------------------------------------|
+| :type      | String or Symbol | resource type; *default* `:records`    |
+| :params    | search options hash; *default* `{}`                       |
+
+##### params
+
+| param.keys | Description                                        |
+|------------|----------------------------------------------------|
+| :rq        | search query hash, default `{}`                    |
+| :limit     | how many records to return in total, default `100` |
+| :offset    | from which record to start, default `0`            |
+
+```ruby
+require "idigbio_client"
+
+# specimen records search
+params = { rq: { genus: "acer" }, limit: 15 }
+IdigbioClient.search(type: :records, params: params)
+
+# using non-default type
+IdigbioClient.search(type: :mediarecords, params: params)
+```
+### Show
+
+#### Method: `IdigbioClient.show(uuid)`
+
+Takes uuid, returns record associated with UUID. Record can be of any type.
+
+| Parameters | Type   | Description |
+|------------|--------|-------------|
+| uuid       | String | UUID        |
+
+
+```ruby
+require "idigbio_client"
+
+IdigbioClient.show("1c29be70-24e7-480b-aab1-61224ded0f34")
+```
+
+### Stats
+
+#### Method: `IdigbioClient.count(opts)`
+
+Returns the number of records of a specified type
+
+| opts.keys  | Type             | Description                            |
+|------------|------------------|----------------------------------------|
+| :type      | String or Symbol | resource type; *default* `:records`    |
+| :params    | search options hash; *default* `{}`                       |
+
+```ruby
+require "idigbio_client"
+
+IdigbioClient.count
+IdigbioClient.count(type: :recordsets)
+IdigbioClient.count(type: :mediarecords, params: { rq: { genus: "acer" } })
+```
+
+Development
+-----------
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, 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` to create a git tag for the version, push git
+commits and tags, and push the `.gem` file to
+[rubygems.org][rubygems].
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/idigbio_client/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 a new Pull Request
+
+Copyright
+---------
+
+Authors -- [Greg Traub][greg], [Dmitry Mozzherin][dimus]
+
+Copyright (c) 2015 [Greg Traub][greg], [Dmitry Mozzherin][dimus]
+See [LICENSE][license] for details.
+
+
+[gem_badge]: https://badge.fury.io/rb/idigbio_client.svg
+[gem_link]: http://badge.fury.io/rb/idigbio_client
+[ci_badge]: https://secure.travis-ci.org/GlobalNamesArchitecture/idigbio_client.svg
+[ci_link]: http://travis-ci.org/GlobalNamesArchitecture/idigbio_client
+[cov_badge]: https://coveralls.io/repos/GlobalNamesArchitecture/idigbio_client/badge.svg?branch=master
+[cov_link]: https://coveralls.io/r/GlobalNamesArchitecture/idigbio_client?branch=master
+[code_badge]: https://codeclimate.com/github/GlobalNamesArchitecture/idigbio_client/badges/gpa.svg
+[code_link]: https://codeclimate.com/github/GlobalNamesArchitecture/idigbio_client
+[dep_badge]: https://gemnasium.com/GlobalNamesArchitecture/idigbio_client.png
+[dep_link]: https://gemnasium.com/GlobalNamesArchitecture/idigbio_client
+[api]: https://www.idigbio.org/wiki/index.php/IDigBio_API
+[inspect]: #inspect
+[search]: #search
+[show]: #show
+[stats]: #stats
+[rubygems]: https://rubygems.org
+[license]: https://github.com/GlobalNamesArchitecture/idigbio-ruby-client/blob/master/LICENSE
+[greg]: https://github.com/gete76
+[dimus]: https://github.com/dimus

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+require "rubocop/rake_task"
+
+RSpec::Core::RakeTask.new(:rspec) do |rspec|
+  rspec.pattern = "spec/**/*_spec.rb"
+end
+
+RuboCop::RakeTask.new
+
+task default: [:rubocop, :rspec]

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "idigbio_client"
+
+# 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

data/bin/setup

@@ -0,0 +1,7 @@
+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/exe/idigbio

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+#!/usr/bin/env ruby
+
+require "trollop"
+
+SUB_COMMANDS = %w(search)
+global_opts = Trollop.options do
+  banner "Client to iDibBio API \n" \
+         "Usage:\n" \
+         "idigbio search [opts]\n" \
+         "--------------------------"
+
+  stop_on SUB_COMMANDS
+end
+
+cmd = ARGV.shift
+cmd_opts = case cmd
+           when "search"
+             Trollop.options do
+               opt(:method,
+                   "HTTP method: get or post",
+                   short: "-m",
+                   default: "post")
+             end
+           else
+             Trollop.die "unknown subcommand #{cmd.inspect}"
+           end
+
+puts "Global options: #{global_opts.inspect}"
+puts "Subcommand: #{cmd.inspect}"
+puts "Subcommand options: #{cmd_opts.inspect}"
+puts "Remaining arguments: #{ARGV.inspect}"

data/idigbio_client.gemspec

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+# coding: utf-8
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "idigbio_client/version"
+
+Gem::Specification.new do |gem|
+  gem.name          = "idigbio_client"
+  gem.version       = IdigbioClient::VERSION
+  gem.authors       = ["Greg T.", "Dmitry Mozzherin"]
+  gem.email         = ["dmozzherin@gmail.com"]
+
+  gem.summary       = "Ruby wrapper for iDigBio API"
+  gem.description   = "Ruby wrapper for iDigBio API"
+  gem.homepage      = "https://github.com/GlobalNamesArchitecture/idigbio-ruby-client"
+
+  gem.files         = `git ls-files -z`.split("\x0").
+    reject { |f| f.match(%r{^(test|spec|features)/}) }
+  gem.bindir        = "exe"
+  gem.executables   = gem.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  gem.require_paths = ["lib"]
+  gem.add_dependency "rest-client", "~> 1.8"
+  gem.add_dependency "trollop", "~> 2.1"
+
+  gem.add_development_dependency "bundler", "~> 1.7"
+  gem.add_development_dependency "rake", "~> 10.0"
+  gem.add_development_dependency "rspec", "~> 3.2"
+  gem.add_development_dependency "rubocop", "~> 0.31"
+  gem.add_development_dependency "coveralls", "~> 0.8"
+end

data/lib/idigbio_client.rb

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+require "json"
+require "logger"
+require "rest_client"
+require "idigbio_client/version"
+require "idigbio_client/helper"
+require "idigbio_client/search"
+
+# Ruby wrapper for iDigBio API
+module IdigbioClient
+  URL = "https://beta-search.idigbio.org/v2/"
+  MAX_LIMIT = 100_000
+  DEFAULT_LIMIT = 100
+  HEADERS = { content_type: :json, accept: :json }
+  extend Helper
+
+  class << self
+    def search(opts)
+      Search.search(opts)
+    end
+
+    def logger
+      @logger ||= Logger.new($stdout)
+    end
+
+    def show(uuid)
+      query(path: "view/#{uuid}", method: :get)
+    end
+
+    def types
+      %w(records mediarecords recordsets publishers)
+    end
+
+    def count(opts = {})
+      opts = { type: "records", params: {} }.merge(opts)
+      type = normalize_type(opts[:type])
+      res = query(path: "summary/count/#{type}/", params: opts[:params])
+      res ? res[:itemCount] : nil
+    end
+
+    def fields(type = nil)
+      types = type ? [normalize_type(type)] : IdigbioClient.types
+      types.each_with_object({}) do |t, res|
+        res[t.to_sym] = query(path: "meta/fields/#{t}", method: :get)
+      end
+    end
+  end
+end

data/lib/idigbio_client/helper.rb

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+module IdigbioClient
+  # Private internal methods
+  module Helper
+    def query(opts)
+      url, params = url_params(opts)
+      resp = post?(opts[:method]) ? post(url, params) : get(url, params)
+      resp = JSON.parse(resp.body, symbolize_names: true) if resp
+      sleep(0.3)
+      block_given? ? yield(resp) : resp
+    end
+
+    def url_params(opts)
+      opts = { method: "post" }.merge(opts)
+      url = URL + opts[:path]
+      params = HEADERS.merge(params: opts[:params].to_json)
+      [url, params]
+    end
+
+    def post?(method)
+      !method.to_s.match(/get/i)
+    end
+
+    def post(url, params)
+      request(:post, url, params)
+    end
+
+    def get(url, params)
+      params[:query] = params.delete(:params)
+      request(:get, url, params)
+    end
+
+    def request(method, url, params)
+      RestClient.send(method, url, params) do |resp, _req, _res|
+        resp.code == 200 ? resp : nil
+      end
+    end
+
+    def normalize_type(type)
+      type = type.to_s
+      return type if IdigbioClient.types.include?(type)
+      sym_types = types.map { |t| ":#{t}" }.join(", ")
+      fail "Unknown type :#{type}. Types: #{sym_types}"
+    end
+
+    def symbolize(h)
+      h.keys.each do |k|
+        sym = k.to_sym
+        h[sym] = h.delete(k)
+        symbolize(h[sym]) if h[sym].is_a? Hash
+      end
+    end
+  end
+end

data/lib/idigbio_client/search.rb

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+module IdigbioClient
+  # Performs Searh over iDigBio Resources
+  module Search
+    extend IdigbioClient::Helper
+
+    class << self
+      def search(opts)
+        opts = prepare_opts(opts)
+        orig_offset = opts[:params][:offset]
+        resp = paginate(opts)
+        resp[:items] = resp[:items][0...(opts[:params][:limit] - orig_offset)]
+        block_given? ? yield(resp) : resp
+      end
+
+      private
+
+      def paginate(opts)
+        items = []
+        params = opts[:params]
+        while params[:items_to_go].nil? || params[:items_to_go] > 0
+          resp = IdigbioClient.query(opts)
+          items += resp[:items] if resp[:itemCount] > 0
+          adjust_params(resp, params)
+        end
+        resp[:items] = items
+        resp
+      end
+
+      def prepare_opts(opts)
+        symbolize(opts)
+        opts = { type: :records, method: :post, params: {} }.merge(opts)
+        opts[:params] = { rq: {}, limit: DEFAULT_LIMIT, offset: 0, fields: [],
+                          fields_exclude: [], sort: [] }.merge(opts[:params])
+        opts[:path] = prepare_path(opts[:type])
+        opts
+      end
+
+      def prepare_path(type)
+        type = normalize_type(type)
+        type.gsub!("mediarecords", "media")
+        "search/#{type}/"
+      end
+
+      def adjust_params(resp, params)
+        logger_write(resp, params)
+        params[:items_to_go] ||=
+          [MAX_LIMIT, resp[:itemCount], params[:limit]].min - params[:offset]
+        params[:offset] += resp[:items].size
+        params[:items_to_go] -= resp[:items].size
+      end
+
+      def logger_write(resp, params)
+        s = params[:offset] + 1
+        e = [params[:offset] + resp[:items].size, params[:limit]].min
+        IdigbioClient.logger.info(
+          "Processed items #{s}-#{e} out of #{params[:limit]}"
+        )
+      end
+    end
+  end
+end

data/lib/idigbio_client/version.rb

@@ -0,0 +1,8 @@
+# Ruby wrapper for iDigBio API
+module IdigbioClient
+  VERSION = "0.1.0"
+
+  def self.version
+    VERSION
+  end
+end

metadata

@@ -0,0 +1,160 @@
+--- !ruby/object:Gem::Specification
+name: idigbio_client
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Greg T.
+- Dmitry Mozzherin
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2015-05-20 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  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'
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.31'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.31'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+description: Ruby wrapper for iDigBio API
+email:
+- dmozzherin@gmail.com
+executables:
+- idigbio
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".rubocop.yml"
+- ".travis.yml"
+- CHANGELOG.md
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- exe/idigbio
+- idigbio_client.gemspec
+- lib/idigbio_client.rb
+- lib/idigbio_client/helper.rb
+- lib/idigbio_client/search.rb
+- lib/idigbio_client/version.rb
+homepage: https://github.com/GlobalNamesArchitecture/idigbio-ruby-client
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.3
+signing_key: 
+specification_version: 4
+summary: Ruby wrapper for iDigBio API
+test_files: []