sylfy 0.0.2 → 0.1.0

data/lib/sylfy/service/ebisoap.rb

@@ -0,0 +1,55 @@
+# 
+# Systems biology library for Ruby (Sylfy)
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# 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"
+
+
+require 'sylfy/service/soapwsdl'
+
+module Sylfy
+    # A module supports as interfaces for web services
+    module Service
+        module ChEBI
+            class SOAP < Sylfy::Service::SOAPWSDL
+                def initialize(options = {})
+                    super('http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl', options)
+                end
+                
+            end
+            
+            module_function
+			
+			# Search ChEBI database using InChI
+			#
+			# == Parameters:
+			# inchi::
+			#   inchi string to search
+			def idbyinchi(inchi)
+                output = Sylfy::Service::ChEBI::SOAP.new.get_structure_search(structure: Rubabel[inchi, :inchi].to_s(:can), type: 'SMILES', structureSearchCategory: 'IDENTITY')
+                return output != nil ? ["urn:miriam:chebi:#{output[:list_element][:chebi_id]}"] : []
+			end
+			
+        end
+        
+        module Miriam
+            class SOAP < Sylfy::Service::SOAPWSDL
+                def initialize(options = {})
+                    super('http://www.ebi.ac.uk/miriamws/main/MiriamWebServices?wsdl', options)
+                end
+            end
+        end
+    end
+end
+
+
+#p Sylfy::Service::PubChem::REST.compound('QIQXTHQIDYTFRH-UHFFFAOYSA-N', :inchikey, 'xrefs/SBURL')["InformationList"]["Information"][0]["SBURL"]
+#p Sylfy::Service::ChEBI::SOAP.new().get_complete_entity(chebiId: "CHEBI:15377")
+#p Sylfy::Service::Miriam::SOAP.new().get_official_data_type_uri("nickname" => "ChEBI")
+#p Sylfy::Service::Miriam::SOAP.new().convert_url(string: "urn:miriam:chebi:CHEBI:28842")
+#p Sylfy::Service::Miriam::SOAP.new().get_official_data_type_uri(nickname: "chebi")
+#p Sylfy::Service::Miriam::SOAP.new().get_miriam_uri(uri: "http://www.ebi.ac.uk/chebi/#CHEBI:17891")

data/lib/sylfy/service/ensemblrest.rb

@@ -0,0 +1,64 @@
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'open-uri'
+require 'net/http'
+require 'rexml/document'
+require 'json'
+require 'yaml'
+
+require 'sylfy/service/ensemblrest/xrefs.rb'
+require 'sylfy/service/ensemblrest/archive.rb'
+require 'sylfy/service/ensemblrest/comparative.rb'
+
+module Sylfy
+	
+	module Service
+		
+		module ENSEMBL
+			module REST
+			
+				BASEURI = URI.parse("http://beta.rest.ensembl.org")
+				HTTP = Net::HTTP.new(BASEURI.host, BASEURI.port)
+				
+				module_function
+				
+				# internal method supporting all ENSEMBLREST service
+				#
+				# @param get_path [String] service get_path
+				#
+				# @param option_type [Array] list of option type of service
+				#
+				# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+				#	
+				# @return [array of Hash] results
+				#
+				def service(get_path, option_type = [], option={})
+					
+					optionList = []
+						
+					option.each do |k, v|
+						optionList.push("#{k}=#{v}") if option_type.include?(k.to_sym)
+					end
+					
+					
+					get_path += "?#{optionList.join(";")}" if !optionList.empty?
+					
+					request = Net::HTTP::Get.new(get_path, {'Content-Type' => option.has_key?('content-type') ? option['content-type'] : 'application/json'})
+					response = HTTP.request(request)
+					
+					if response.code != "200"
+						#raise ParameterError, "Invalid response: #{response.code}"
+					else
+						if option.has_key?('content-type') && option['content-type'] != 'application/json'
+							return response.body
+						else
+							return JSON.parse(response.body)
+						end
+					end
+					
+				end
+			end
+		end
+		
+	end
+end

data/lib/sylfy/service/ensemblrest/archive.rb

@@ -0,0 +1,35 @@
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'json'
+
+module Sylfy
+	
+	module Service
+	
+		module ENSEMBLREST
+			module REST
+				module Archive
+					
+					SERVICENAME = 'archive'
+					
+					module_function
+					
+					# Uses the given identifier to return the archived sequence
+					#
+					# @param id [String] The stable identifier of the entity you wish to retrieve overlapping features
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/archive_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def id(id, option = {})
+						option_type = [:callback]
+						get_path = "/#{SERVICENAME}/id/#{id}"
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+					
+				end
+			end
+        end
+    end
+end

data/lib/sylfy/service/ensemblrest/comparative.rb

@@ -0,0 +1,146 @@
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'json'
+
+module Sylfy
+	
+	module Service
+	
+		module ENSEMBL
+			module REST
+				module Alignment
+					
+					SERVICENAME = 'alignment'
+					
+					module_function
+					
+					# Retrieves genomic alignments as separate blocks based on its location
+					#
+					# @param species [String] Registry name/aliases used to restrict searches by
+					#
+					# @param region [String] The region to retrieve sequence for. A maximum of
+					# 10Mb is allowed to be requested at any one time
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def block(species, region, option = {})
+						option_type = [:callback, :compact, :compara, :display_species_set, :mask, :method, :species_set, :species_set_group]
+						get_path = "/#{SERVICENAME}/block/region/#{species}/#{region}"
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+					
+					# Retrieves genomic alignments as a single slice based on its location
+					#
+					# @param species [String] Registry name/aliases used to restrict searches by
+					#
+					# @param region [String] The region to retrieve sequence for. A maximum of
+					# 10Mb is allowed to be requested at any one time
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def slice(species, region, option = {})
+						option_type = [:callback, :compact, :compara, :display_species_set, :expanded, :mask, :method, :overlap, :species_set, :species_set_group]
+						get_path = "/#{SERVICENAME}/slice/region/#{species}/#{region}"
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+					
+				end
+				
+				module Genetree
+					
+					SERVICENAME = 'genetree'
+					
+					module_function
+	
+					# Retrieves Gene Tree dumps for a given Gene Tree stable identifier
+					#
+					# @param id [String] Ensembl GeneTree ID
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def id(id, option = {})
+						option_type = [:aligned, :nh_format , :sequence]
+						get_path = "/#{SERVICENAME}/id/#{id}"
+						option['Content-Type'] = 'text/x-nh'
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+					
+					# Retrieves the Gene Tree that contains the given stable identifier
+					#
+					# @param id [String] Ensembl gene ID
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def member(id, option = {})
+						option_type = [:db_type, :object_type , :species]
+						get_path = "/#{SERVICENAME}/member/id/#{id}"
+						option['Content-Type'] = 'text/x-phyloxml+xml'
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+					
+					# Retrieves a Gene Tree containing the Gene identified by the given symbol
+					#
+					# @param species [String] Registry name/aliases used to restrict searches by
+					#
+					# @param symbol [String] The external name/symbol to search for
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def symbol(species, symbol, option = {})
+						option_type = [:db_type, :external_db, :object_type]
+						get_path = "/#{SERVICENAME}/member/symbol/#{species}/#{symbol}"
+						option['Content-Type'] = 'text/x-phyloxml+xml'
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+				end
+				
+				module Homology
+					
+					SERVICENAME = 'homology'
+					
+					module_function
+	
+					# Retrieves homology information by ensembl gene id
+					#
+					# @param id [String] Ensembl GeneTree ID
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def id(id, option = {})
+						option_type = [:aligned, :callback, :format, :sequence, :species,  :target_species, :target_taxon, :type]
+						get_path = "/#{SERVICENAME}/id/#{id}"
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+					
+					# Retrieves homology information by symbol
+					#
+					# @param species [String] Registry name/aliases used to restrict searches by
+					#
+					# @param symbol [String] The external name/symbol to search for
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def symbol(species, symbol, option = {})
+						option_type = [:aligned, :callback, :compara, :external_db, :format, :sequence, :target_species, :target_taxon, :type]
+						get_path = "/#{SERVICENAME}/symbol/#{species}/#{symbol}"
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+				end
+			end
+		end
+    end
+end

data/lib/sylfy/service/ensemblrest/xrefs.rb

@@ -0,0 +1,73 @@
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'json'
+
+module Sylfy
+	
+	module Service
+	
+		module ENSEMBL
+			module REST
+			
+				module Xrefs
+					
+					SERVICENAME = 'xrefs'
+					
+					module_function
+					
+					# Perform lookups of Ensembl Identifiers and retrieve their external cross references
+					# in other databases
+					#
+					# @param id [String] ENSEMBL id
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def id(id, option = {})
+						option_type = [:all_levels, :callback, :db_type, :external_db, :object_type, :species]
+						get_path = "/#{SERVICENAME}/id/#{id}"
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+					
+					# Performs a lookup based upon the primary accession or display label of an external
+					# reference and returning the information we hold about the entry
+					#
+					# @param species [String] Registry name/aliases used to restrict searches by
+					#
+					# @param name [String] The external name/primary accession to search for
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def name(species, name, option = {})
+						option_type = [:callback, :db_type, :external_db]
+						get_path = "/#{SERVICENAME}/name/#{species}/#{name}"
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+					
+					# Looks up an external symbol and returns all Ensembl objects linked to it.
+					# This can be a display name for a gene/transcript/translation, a synonym or an
+					# externally linked reference. If a Gene's transcript is linked to the supplied
+					# symbol the service will return both Gene and Transcript (it supports transient
+					# links).
+					#
+					# @param species [String] Registry name/aliases used to restrict searches by
+					#
+					# @param symbol [String] The external name/symbol to search for
+					#
+					# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+					#	
+					# @return [array of Hash] results
+					#
+					def symbol(species, symbol, option = {})
+						option_type = [:callback, :db_type, :external_db, :object_type]
+						get_path = "/#{SERVICENAME}/symbol/#{species}/#{symbol}"
+						return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
+					end
+				end
+			end
+        end
+    end
+end

data/lib/sylfy/service/hgncrest.rb

@@ -0,0 +1,52 @@
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'open-uri'
+require 'net/http'
+require 'rexml/document'
+require 'json'
+require 'yaml'
+
+module Sylfy
+	
+	module Service
+		
+		module ENSEMBL
+            
+			module REST
+				
+				BASEURI = URI.parse('http://rest.genenames.org')
+				HTTP = Net::HTTP.new(BASEURI.host, BASEURI.port)
+				
+				module_function
+				# internal method supporting all ENSEMBLREST service
+				#
+				# @param get_path [String] service get_path
+				#
+				# @param option_type [Array] list of option type of service
+				#
+				# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
+				#	
+				# @return [array of Hash] results
+				#
+				def info()
+					request = Net::HTTP::Get.new(get_path, {'Content-Type' => option.has_key?('content-type') ? option['content-type'] : 'application/json'})
+					response = HTTP.request(request)
+					
+					if response.code != "200"
+						#raise ParameterError, "Invalid response: #{response.code}"
+					else
+						#return YAML::dump(JSON.parse(response.body))
+						if option.has_key?('content-type') && option['content-type'] != 'application/json'
+							return response.body
+						else
+							return JSON.parse(response.body)
+						end
+					end
+				end
+			end
+			
+		end
+		
+	end
+	
+end

data/lib/sylfy/service/keggrest.rb

@@ -1,7 +1,3 @@
-# 
-# UniSysDB library in Ruby
-# Copyright (C) 2012
-#
 # @author Natapol Pornputtapong <natapol@chalmers.se>
 #
 require 'open-uri'
@@ -11,6 +7,7 @@ require 'rexml/document'
 
 require 'sylfy/service/keggrest/conv'
 require 'sylfy/service/keggrest/find'
+require 'sylfy/service/keggrest/get'
 require 'sylfy/service/keggrest/link'
 require 'sylfy/service/keggrest/list'
 
@@ -18,16 +15,14 @@ module Sylfy
 	
 	module Service
 		
-		
-		# http://rest.kegg.jp/<operation>/<argument>/<argument2 or option>
-		# <operation> = info | list | find | get | conv | link
-		# <argument> = <database> | <dbentries>
-		
+		# interface to KEGG API
+		# {http://www.kegg.jp/kegg/rest/keggapi.html}
+		# info | list | find | get | conv | link
 		module KEGGREST
 			
-			@@baseuri = "http://rest.kegg.jp"
+			BASEURI = "http://rest.kegg.jp"
 			
-			@@db = [:pathway, :brite, :module, :disease, :drug, :environ, 
+			DB = [:pathway, :brite, :module, :disease, :drug, :environ, 
 					:ko, :genome, :compound, :glycan, :reaction, :rpair, 
 					:rclass, :enzyme, :genomes, :genes, :ligand, :kegg, :organism]
 			
@@ -39,12 +34,4 @@ module Sylfy
 	end
 end
 
-#require '../unisys.rb'
-
-#p Unisys::Service::RESTKegg.list('hsa:10458+ece:Z5100')
-#p Unisys::Service::RESTKegg.find(:genes, 'shiga+toxin')
-#p Unisys::Service::RESTKegg.conv('hsa:10458+ece:Z5100','ncbi-gi')
-#p Unisys::Service::RESTKegg.get(:G00092)
-#Unisys::Service::RESTKegg.getSmallMolecule(:G00092)
-#p Unisys::Service::RESTKegg.link('hsa:10458+ece:Z5100', 'pathway')