hgncrest 1.0.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 9c2d7607a23c339f457bbdaaa0a5472ecea23253
+  data.tar.gz: 4e4dc696193506888f0e29c81761c5a6bad2258f
+SHA512:
+  metadata.gz: d5a43b9ed70e6d0dc734c8efbd728982e65652651470cfb5d4ffe354169cdd679a3b6435aa31a6d7af4db3567cc51a51df20db7b0f6d9c1e33f3111991c5aeb1
+  data.tar.gz: 5e47c9c6113b09546ea122cdb915282db8cacccb910a0a640d888aac058f43a6a3eb6c2d504e9af13b2506ee8d62fb78f2a9bd1edc95ab24743476de015367c2

data/hgncrest.gemspec

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+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "hgncrest/version"
+
+Gem::Specification.new do |s|
+    s.name          = 'hgncrest'
+    s.version       = HGNCREST::VERSION
+    s.date          = Time.now.strftime("%Y-%m-%d")
+    s.platform      = Gem::Platform::RUBY
+    
+    s.summary       = "HGNC REST Ruby API"
+    s.description   = "HGNC REST Ruby API"
+    s.authors       = ["Natapol Pornputtapong"]
+    s.email         = 'natapol.por@gmail.com'
+
+    s.homepage      = 'http://rubygems.org/gems/hgncrest'
+    s.license       = 'GPL'
+    
+    
+    s.files         = `git ls-files`.split("\n")
+    s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+    s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+    s.require_paths = ["lib"]
+    
+
+end

data/lib/hgncrest/connect.rb

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+# 
+# Bio-ensemblrest
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module HGNCREST
+	
+	@@url = URI.parse('http://rest.genenames.org')
+	@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
+	@@info = nil
+	
+	module_function
+	
+	# Connect to specific URL
+	# 
+	# @param [String] Service URL
+	def connect(url)
+		@@url = URI.parse(url)
+		@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
+	end
+	
+	# Get response
+	# 
+	# @param [String] Specific service path
+	# @return [JSON] request body
+	def get(get_path)
+		request = Net::HTTP::Get.new(get_path, {'Accept' => 'application/json'})
+		response = @@http_connect.request(request)
+		if response.code == "200"
+			return JSON.parse(response.body)
+		else
+			raise "Invalid response: #{response.code}"
+		end
+	end
+	
+	# Download service information
+	def dl_info
+		@@info = HGNCREST::get('/info') if @@info == nil
+	end
+	
+	# Return service information
+	# 
+	# @param [String] Specific service path
+	# @return [JSON] request body
+	def info
+		HGNCREST::dl_info
+		return @@info
+	end
+	
+	# Return a list containing the fields that can be used to fetch and search records
+	# 
+	# @return [Array] searchableFields
+	def searchableFields
+		HGNCREST::dl_info
+		return @@info["searchableFields"]
+	end
+	
+	# Return all the fields that could possibly be returned within a fetch request
+	# 
+	# @return [Array] storedFields
+	def storedFields
+		HGNCREST::dl_info
+		return @@info["storedFields"]
+	end
+	
+end
+

data/lib/hgncrest/fetch.rb

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+# 
+# Bio-ensemblrest
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module HGNCREST
+	
+	@@fetch_cache = {}
+	
+	module_function
+	
+	# Provide search request for detail please follow http://www.genenames.org/help/rest-web-service-help#Content_type
+	# 
+	# @param [String] query string
+	# @param [String, Symbol] specific field to fetch for. If nil, fetch based on all fields
+	# 
+	# @return [Array] request body
+	def fetch(query, field = nil)
+		if @@fetch_cache.has_key?(query)
+			return @@fetch_cache[query]
+		else
+			result = HGNCREST.get("/fetch#{field == nil || field.empty? ? '' : "/#{field.to_s.downcase}"}/#{URI.escape(query)}")['response']['docs']
+			@@fetch_cache[query] = result
+			return result
+		end
+	end
+	
+	# Provide id conversion regarded to HGNC database
+	# 
+	# @param [String, Symbol] query string
+	# @param [String, Symbol] convert from specified field as in searchableFields
+	# @param [String, Symbol] convert to specified field as in storedFields
+	# 
+	# @return [Array] id
+	def convert(query, from, to)
+		HGNCREST::fetch(query, from)[0][to.to_s.downcase]
+	end
+end

data/lib/hgncrest/search.rb

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+# 
+# Bio-ensemblrest
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module HGNCREST
+	
+	@@search_cache = {}
+	
+	module_function
+	
+	# Provide search request for detail please follow http://www.genenames.org/help/rest-web-service-help#Content_type
+	# 
+	# @param [String] query string
+	# @param [String, Symbol] specific field to search for. If nil, search all fields
+	# 
+	# @return [Array] request body
+	def search(query, field = nil)
+		if @@search_cache.has_key?(query)
+			return @@search_cache[query]
+		else
+			result = HGNCREST.get("/search#{field == nil || field.empty? ? '' : "/#{field.to_s.downcase}"}/#{URI.escape(query)}")['response']['docs']
+			@@search_cache[query] = result
+			return result
+		end
+	end
+	
+end

data/lib/hgncrest/version.rb

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+# 
+# Exodus
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+
+module HGNCREST
+	VERSION = "1.0.0"
+end

data/lib/hgncrest.rb

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+# 
+# Bio
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+$: << File.join(File.expand_path(File.dirname(__FILE__)))
+
+#Internal library
+require 'bio'
+require 'open-uri'
+require 'net/http'
+require 'uri'
+require 'json'
+
+require 'hgncrest/version'
+require 'hgncrest/connect'
+require 'hgncrest/fetch'
+require 'hgncrest/search'
+
+#p HGNCREST::storedFields
+#p HGNCREST::searchableFields
+#p HGNCREST::search('BRAF')
+#p HGNCREST::fetch('BRAF', :symbol)
+#p HGNCREST::convert('BRAF', :symbol, :entrez_id)

metadata

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+--- !ruby/object:Gem::Specification
+name: hgncrest
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- Natapol Pornputtapong
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-04-08 00:00:00.000000000 Z
+dependencies: []
+description: HGNC REST Ruby API
+email: natapol.por@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- hgncrest.gemspec
+- lib/hgncrest.rb
+- lib/hgncrest/connect.rb
+- lib/hgncrest/fetch.rb
+- lib/hgncrest/search.rb
+- lib/hgncrest/version.rb
+homepage: http://rubygems.org/gems/hgncrest
+licenses:
+- GPL
+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: 2.0.14
+signing_key: 
+specification_version: 4
+summary: HGNC REST Ruby API
+test_files: []
+has_rdoc: