gene_names 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 9d6cef66a7dcf6fe253dcde653c2d70cd8e77a24
+  data.tar.gz: 6882686de1ba7e41e89ea8b6c64533212a448653
+SHA512:
+  metadata.gz: 7723a539fb9c710be56bc454ef4eb779d22555a5ac1c19e1867beb807a2e8acf09b930b67ac35efb6a4359075b56fc1a7f8757649411163677a2f01022948b80
+  data.tar.gz: b589f0118d050d95ab2be2fff8ddcb7723f95c891e5891c3e5fc1dba7e3fe78f5671323226a6b6ab171d2546f5498379de8267c15826301ac27faad2110521e8

data/.gitignore

@@ -0,0 +1,22 @@
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in gene_names.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2014 Eric Harrison
+
+MIT License
+
+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 +1,33 @@
+GeneNames
+====================
+
+A sall little gem used for fetching gene information from genenames.org's REST api
+
+## Installation
+``` bash
+gem install gene_names
+```
+
+## Usage
+```ruby
+  require 'gene_names'
+  gene = GeneNames.fetch('TOP2A')
+  gene.inspect
+```
+
+## Copyright
+
+Copyright (c) 2014 SmashTank Apps, LLC.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.

data/Rakefile

@@ -0,0 +1,2 @@
+require "bundler/gem_tasks"
+

data/gene_names.gemspec

@@ -0,0 +1,23 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'gene_names/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "gene_names"
+  spec.version       = GeneNames::VERSION
+  spec.authors       = ["Eric Harrison", "SmashTank Apps"]
+  spec.email         = ["eharrison@smashtankapps.com"]
+  spec.summary       = %q{Gem for access to genenames.org api}
+  spec.description   = %q{}
+  spec.homepage      = "http://github.com/smashtank/gene_names"
+  spec.license       = "MIT"
+
+  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.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+end

data/lib/gene_names.rb

@@ -0,0 +1,7 @@
+require "gene_names/version"
+require "gene_names/constants"
+require "gene_names/http"
+require "gene_names/record"
+
+module GeneNames
+end

data/lib/gene_names/constants.rb

@@ -0,0 +1,3 @@
+module GeneNames
+  SERVER = 'http://rest.genenames.org'
+end

data/lib/gene_names/http.rb

@@ -0,0 +1,89 @@
+require 'net/http'
+require 'uri'
+require 'json'
+
+module GeneNames
+  class HTTP
+    class InvalidResponse < StandardError; end;
+    def self.fetch(value, type)
+      do_request('/' + ['',:fetch, type, value].collect(&:to_s).join('/'))['response']['docs'].collect{|doc| GeneNames::Record.new(doc)}
+    end
+
+    def self.info
+      do_request('/info')
+    end
+
+    def self.search
+      #TODO
+    end
+
+    def self.searchable_fields=(*fields)
+      @searchable_fields = fields
+    end
+
+    def self.searchable_fields
+      return @search_fields || load_searchable_fields
+    end
+
+    def self.stored_fields=(*fields)
+      @searchable_fields = fields
+    end
+
+    def self.stored_fields
+      return @stored_fields || load_stored_fields
+    end
+
+    private
+
+    def self.load_searchable_fields
+      self.searchable_fields = self.info['searchableFields']
+    end
+
+    def self.load_stored_fields
+      self.searchable_fields = self.info['storedFields']
+    end
+
+    def self.do_request(path, response_type = :json)
+      http = build_http
+      response = get_response(http, path, response_type)
+      return parse_response(response)
+    end
+
+    def self.build_http
+      url = URI.parse(GeneNames::SERVER)
+      Net::HTTP.new(url.host, url.port)
+    end
+
+    def self.get_response(http, path, response_type)
+      response = http.request(self.build_request(path, response_type))
+      raise InvalidResponse, "Invalid response: #{response.code}" unless response.code == '200'
+      return response
+    end
+
+    def self.build_request(path, response_type)
+      Net::HTTP::Get.new(path, {'Accept' => accept_for_type(response_type)})
+    end
+
+    def self.parse_response(response)
+      return case response.content_type
+      when 'application/json'
+        JSON.parse(response.body)
+      when 'text/xml'
+        #TODO
+      else
+        raise "Unknown content type: '#{response.content_type.to_s}'"
+      end
+    end
+
+    def self.accept_for_type(response_type)
+      case response_type
+      when :json, 'json'
+        'application/json'
+      when :xml, xml
+        'text/xml'
+      else
+        raise "Unknown response type: '#{response_type.to_s}'"
+      end
+    end
+  end
+end

data/lib/gene_names/record.rb

@@ -0,0 +1,19 @@
+module GeneNames
+  class Record
+    GeneNames::HTTP.stored_fields.each do |f|
+      attr_accessor f.to_sym rescue nil
+    end
+
+    def initialize(params = {})
+      params.map{|k,v| self.send(k + '=', v)}
+    end
+
+    def self.find_all(value, type = :symbol)
+      GeneNames::HTTP.fetch(value, type)
+    end
+
+    def chromosome
+      self.location.gsub(/^(\d+).*$/, '\1')
+    end
+  end
+end

data/lib/gene_names/version.rb

@@ -0,0 +1,3 @@
+module GeneNames
+  VERSION = "0.0.1"
+end

metadata

@@ -0,0 +1,84 @@
+--- !ruby/object:Gem::Specification
+name: gene_names
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Eric Harrison
+- SmashTank Apps
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-07-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  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: ''
+email:
+- eharrison@smashtankapps.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- gene_names.gemspec
+- lib/gene_names.rb
+- lib/gene_names/constants.rb
+- lib/gene_names/http.rb
+- lib/gene_names/record.rb
+- lib/gene_names/version.rb
+homepage: http://github.com/smashtank/gene_names
+licenses:
+- MIT
+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: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Gem for access to genenames.org api
+test_files: []