sylfy 0.0.2 → 0.1.0

data/lib/sylfy/service/pubchem.rb

@@ -0,0 +1,71 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'open-uri'
+require 'net/http'
+require 'json'
+
+require 'sylfy/service/pubchemrest'
+
+module Sylfy
+	
+	module Service
+		
+		module PubChem
+			
+			module_function
+			
+			# Method for setting inchi data member
+			#
+			# == Parameters:
+			# id::
+			#   LipidMap id to search
+			# :id, :dataPrimarySource, :xrefs, :relations :inchi, :formula, :smiles, :inchiKey :names
+			def idbyinchi(inchi)
+				result = []
+				if inchi =~ /^InChI\=1S\/[A-Za-z0-9]+(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,]+)+$/
+					REST::compound(Rubabel[inchi, :inchi].write(:inchikey), 'inchikey', "cids")["IdentifierList"]["CID"].each {|e| result.push("urn:miriam:pubchem.compound:#{e}")}
+				elsif inchi =~ /^[A-Z]{14}\-[A-Z]{10}(\-[A-N])?/
+					REST::compound(inchi, 'inchikey', "cids")["IdentifierList"]["CID"].each {|e| result.push("urn:miriam:pubchem.compound:#{e}")}
+				end
+				
+				return result
+			end
+			
+			# Method for setting inchi data member
+			#
+			# == Parameters:
+			# id::
+			#   LipidMap id to search
+			# :id, :dataPrimarySource, :xrefs, :relations :inchi, :formula, :smiles, :inchiKey :names
+			def getnames(inchi)
+				result = []
+				inchi = Rubabel[inchi, :inchi].to_s(:inchikey) if inchi =~ /^InChI\=1S\/[A-Za-z0-9]+(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,]+)+$/
+				
+				if inchi =~ /^[A-Z]{14}\-[A-Z]{10}(\-[A-N])?/
+					Sylfy::Service::PubChem::REST.compound(inchi, :inchikey, "property/IUPACName")["PropertyTable"]["Properties"].each {|e| result.push(e["IUPACName"])}
+					Sylfy::Service::PubChem::REST.compound(inchi, :inchikey, :synonyms)["InformationList"]["Information"].each {|e| result += e["Synonym"]}
+				end
+				
+				return result.uniq[0..21]
+			end
+		end
+	end
+end
+
+
+
+#require 'json'
+#require './unisys.rb'
+
+#http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/sids/XML?sids_type=inactive
+
+#p JSON.load(Unisys::Service::RESTPubChem.assay("1000", :aid, :sids, :JSON ,{:sids_type => :inactive}))
+#p JSON.load(Unisys::Service::RESTPubChem.substance("747285", "sourceid/DTP.NCI"))
+#p JSON.load(Unisys::Service::RESTPubChem.compound("2244", :cid, "property/MolecularFormula,CanonicalSMILES,InChI,InChIKey,IUPACName", "JSON"))
+#p Unisys::Service::RESTPubChem.getSmallMolecule(2244, :cid)
+#p Unisys::Service::RESTPubChem.idconv('D00001')
+#p JSON.load(Unisys::Service::RESTPubChem.compound("LMFA08040013", 'xref/RegistryID', "property/MolecularFormula,CanonicalSMILES,InChI,InChIKey,IUPACName", "JSON"))

data/lib/sylfy/service/pubchemrest.rb

@@ -0,0 +1,249 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'open-uri'
+require 'net/http'
+require 'json'
+
+module Sylfy
+	
+	module Service
+		
+		
+		module PubChem
+			
+			module REST
+				@@baseuri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug"
+				@@output_type = [:XML, :ASNT, :ASNB, :JSON, :JSONP, :SDF, :CSV, :PNG, :TXT]
+				@@main_oper = [:record, :aids, :sids, :cids]
+				@@cmp_property = ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "IsomericSMILES", "InChI", "InChIKey", "IUPACName", "XLogP", "ExactMass", \
+							"MonoisotopicMass", "TPSA", "Complexity", "Charge", "HBondDonorCount", "HBondAcceptorCount", "RotatableBondCount", "HeavyAtomCount", \
+							"IsotopeAtomCount", "AtomStereoCount", "DefinedAtomStereoCount", "UndefinedAtomStereoCount", "BondStereoCount", "DefinedBondStereoCount", \
+							"UndefinedBondStereoCount", "CovalentUnitCount", "Volume3D", "XStericQuadrupole3D", "YStericQuadrupole3D", "ZStericQuadrupole3D", "FeatureCount3D", \
+							"FeatureAcceptorCount3D", "FeatureDonorCount3D", "FeatureAnionCount3D", "FeatureCationCount3D", "FeatureRingCount3D", "FeatureHydrophobeCount3D", \
+							"ConformerModelRMSD3D", "EffectiveRotorCount3D", "ConformerCount3D"]
+				@@xref_ns = ['RegistryID', 'RN', 'PubMedID', 'MMDBID', 'ProteinGI', 'NucleotideGI', 'TaxonomyID', 'MIMID', 'GeneID', 'ProbeID', 'PatentID']
+				@@xref_oper = ['RegistryID', 'RN', 'PubMedID', 'MMDBID', 'DBURL', 'SBURL', 'ProteinGI', 'NucleotideGI', 'TaxonomyID', 'MIMID', 'GeneID', 'ProbeID', 'PatentID']
+	
+				@@assay_type = ['all', 'confirmatory', 'doseresponse', 'onhold', 'panel', 'rnai', 'screening', 'summary']
+				
+				#http://pubchem.ncbi.nlm.nih.gov/rest/pug/<input specification>/<operation specification>/[<output specification>][?<operation_options>]
+				
+				#<input specification> = <domain>/<namespace>/<identifiers>
+				#	<domain> = substance | compound | assay | <other inputs>
+				#		compound domain <namespace> = cid | name | smiles | inchi | sdf | inchikey | <structure search> | <xref> | listkey
+				#			<structure search> = {substructure | superstructure | similarity | identity}/{smiles | inchi | sdf | cid}
+				#			<xref> = xref/{RegistryID | RN | PubMedID | MMDBID | ProteinGI | NucleotideGI | TaxonomyID | MIMID | GeneID | ProbeID | PatentID}
+				#		substance domain <namespace> = sid | sourceid/<source name> | sourceall/<source name> | name | <xref> | listkey
+				#			<source name> = any valid PubChem depositor name
+				#		assay domain <namespace> = aid | listkey | type/<assay type> | sourceall/<source name>
+				#			<assay type> = all | confirmatory | doseresponse | onhold | panel | rnai | screening | summary
+				#		<other inputs> = sources/[substance, assay]
+				#	<identifiers> = comma-separated list of positive integers (cid, sid, aid) or identifier strings (source, inchikey, listkey); single identifier string (name, smiles, xref; inchi, sdf by POST only)
+				#	
+				#
+				#compound domain <operation specification> = record | <compound property> | synonyms | sids | cids | aids | assaysummary | classification
+				#	<compound property> = property / [comma-separated list of property tags]
+				#substance domain <operation specification> = record | synonyms | sids | cids | aids | assaysummary | classification
+				#assay domain <operation specification> = record | aids | sids | cids | description | targets/<target type> | <doseresponse> | summary
+				#	target_type = {ProteinGI, ProteinName, GeneID, GeneSymbol}
+				#	<doseresponse> = doseresponse/sid
+				#
+				#
+				#<output specification> = XML | ASNT | ASNB | JSON | JSONP [ ?callback=<callback name> ] | SDF | CSV | PNG | TXT
+				
+				module_function
+				
+				def perform(input, operation = '', output = :JSON, option = nil)
+					
+					option_text = []
+					option.each_pair{|k, v| option_text.push("#{k.to_s}=#{v.to_s}")} if option.class == Hash
+					
+					if @@output_type.include?(output.to_sym)
+						uri = "#{@@baseuri}/#{URI.escape(input, "[] ")}"
+						uri += "/#{operation}" if operation != nil && operation != ''
+						uri += "/#{output}"
+						uri += "?#{option_text.join(',')}" if option_text.length > 0
+						
+						case output.to_sym
+						when :JSON
+							JSON.parse(URI.parse(uri).read().strip())
+						else
+							return URI.parse(uri).read().strip()
+						end
+						
+					else
+						raise Sylfy::Service::ParameterError, "Wrong output type. Should be #{@@output_type.inspect}"
+					end
+					
+				end
+				
+				# Method for setting inchi data member
+				#
+				# == Parameters:
+				# id::
+				#   LipidMap id to search
+				# :id, :dataPrimarySource, :xrefs, :relations :inchi, :formula, :smiles, :inchiKey :names
+				def substance(identifiers, namespace, operation = '', output = :JSON, option = nil)
+					
+					oper = @@main_oper + [:synonyms, :assaysummary, :classification]
+					ns = [:sid, :name, :listkey]
+					
+					tmp_operation = ""
+					
+					if ns.include?(namespace.to_sym)
+						namespace = namespace.to_s
+					else
+						namespace = namespace.to_s.split(/\//)
+						if ['sourceid', 'sourceall'].include?(namespace[0])
+							namespace = namespace.join('/')
+						elsif namespace[0] == 'xref' && @@xref_ns.include?(namespace[1])
+							namespace = namespace[0..2].join('/')
+						else
+							raise ServiceException::ParameterError, "Wrong domain type. Should be #{ns.join(', ')}, \
+								xref/{#{@@xref_ns.join(' | ')}}, \
+								sourceid/<source name> or sourceall/<source name>"
+						end
+					end
+					
+					if oper.include?(operation.to_sym)
+						tmp_operation = operation.to_s
+					else
+						tmp_operation = ""
+					end
+					
+					
+					
+					begin
+						return perform("substance/#{namespace}/#{identifiers.to_s}", tmp_operation, output, option)
+					rescue OpenURI::HTTPError
+						return {}
+					end
+					
+				end
+				
+				# Method for setting inchi data member
+				#
+				# == Parameters:
+				# id::
+				#   LipidMap id to search
+				# :id, :dataPrimarySource, :xrefs, :relations :inchi, :formula, :smiles, :inchiKey :names
+				def compound(identifiers, namespace, operation = '', output = :JSON, option = nil)
+					oper = @@main_oper + [:synonyms, :assaysummary, :classification]
+					ns = [:cid, :name, :smiles, :inchi, :sdf, :inchikey, :listkey]
+					
+					tmp_operation = ""
+					
+					if ns.include?(namespace.to_sym)
+						namespace = namespace.to_s
+					else
+						namespace = namespace.to_s.split(/\//)
+						if ['substructure', 'superstructure', 'similarity', 'identity'].include?(namespace[0]) && ['smiles', 'inchi', 'sdf', 'cid'].include?(namespace[1])
+							namespace = namespace[0..1].join('/')
+						elsif namespace[0] == 'xref' && @@xref_ns.include?(namespace[1])
+							namespace = namespace[0..2].join('/')
+						else
+							raise ServiceException::ParameterError, "Wrong domain type. Should be #{ns.join(', ')}, \
+								xref/{#{@@xref_ns.join(' | ')}} or \
+								{substructure | superstructure | similarity | identity}/{smiles | inchi | sdf | cid}"
+						end
+					end
+					
+					if oper.include?(operation.to_sym)
+						tmp_operation = operation.to_s
+					else
+						operation = operation.to_s.split(/\//)
+						if operation[0] == 'property' #&& @@cmp_property.repeated_permutation(n).include?()
+							tmp_operation = operation[0..1].join('/')
+						elsif operation[0] == 'xrefs' && @@xref_oper.include?(operation[1])
+							tmp_operation = operation[0..1].join('/')
+						else
+							tmp_operation = ""
+						end
+					end
+					
+					begin
+						return perform("compound/#{namespace}/#{identifiers.to_s}", tmp_operation, output, option)
+					rescue OpenURI::HTTPError
+						return {}
+					end
+					
+				end
+				
+				# Method for setting inchi data member
+				#
+				# == Parameters:
+				# id::
+				#   LipidMap id to search
+				# :id, :dataPrimarySource, :xrefs, :relations :inchi, :formula, :smiles, :inchiKey :names
+				def assay(identifiers, namespace, operation = '', output = :JSON, option = nil)
+					oper = @@main_oper + [:description]
+					ns = [:aid, :listkey]
+					
+					tmp_operation = ""
+	
+					if ns.include?(namespace.to_sym)
+						namespace = namespace.to_s
+					else
+						namespace = namespace.split(/\//)
+						if namespace[0] == 'type' && @@assay_type.include?(namespace[1])
+							namespace = namespace[0..1].join('/')
+						elsif namespace[0] == 'sourceall'
+							namespace = namespace[0..1].join('/')
+						else
+							raise ServiceException::ParameterError, "Wrong domain type. Should be #{ns.join(', ')}, \
+								type/{#{@@assay_type.join(' | ')}} or sourceall/<source name>"
+						end
+					end
+					
+					if oper.include?(operation.to_sym)
+						tmp_operation = operation.to_s
+					elsif operation.to_s =~ /^targets\/([\w,]+)/ #target_type = {ProteinGI, ProteinName, GeneID, GeneSymbol}
+						tmp_operation = operation.to_s
+					elsif operation.to_s =~ /^doseresponse\/([\w,]+)/ #doseresponse/sid
+						tmp_operation = operation.to_s
+					else
+						tmp_operation = ""
+					end
+					
+					begin
+						return perform("assay/#{namespace}/#{identifiers.to_s}", tmp_operation, output, option)
+					rescue OpenURI::HTTPError
+						return {}
+					end
+					
+				end
+				
+				# Method for setting inchi data member
+				#
+				# == Parameters:
+				# id::
+				#   LipidMap id to search
+				# :id, :dataPrimarySource, :xrefs, :relations :inchi, :formula, :smiles, :inchiKey :names
+				def idconv(id)
+					return JSON.load(compound(id, 'xref/RegistryID', "cids"))["IdentifierList"]["CID"]
+				end
+				
+				
+			end
+			
+		end
+	end
+end
+
+
+
+#require 'json'
+#require './unisys.rb'
+
+#http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/sids/XML?sids_type=inactive
+
+#p JSON.load(Unisys::Service::RESTPubChem.assay("1000", :aid, :sids, :JSON ,{:sids_type => :inactive}))
+#p JSON.load(Unisys::Service::RESTPubChem.substance("747285", "sourceid/DTP.NCI"))
+#p JSON.load(Unisys::Service::RESTPubChem.compound("2244", :cid, "property/MolecularFormula,CanonicalSMILES,InChI,InChIKey,IUPACName", "JSON"))
+#p Unisys::Service::RESTPubChem.getSmallMolecule(2244, :cid)
+#p Unisys::Service::RESTPubChem.idconv('D00001')
+#p JSON.load(Unisys::Service::RESTPubChem.compound("LMFA08040013", 'xref/RegistryID', "property/MolecularFormula,CanonicalSMILES,InChI,InChIKey,IUPACName", "JSON"))

data/lib/sylfy/service/rest.rb

@@ -0,0 +1,26 @@
+# @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 RESTInclude
+			
+			def resolve(args)
+				#code
+			end
+		end
+        
+	end
+	
+end

data/lib/sylfy/service/soapwsdl.rb

@@ -0,0 +1,78 @@
+# 
+# Systems biology library for Ruby (Sylfy)
+# Copyright::  Copyright (C) 2006
+#              Toshiaki Katayama <k@bioruby.org>
+# Copyright (C) 2012-2013
+#
+# 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 'savon'
+#namespaces = {
+#  "xmlns:v2" => "http://v2.example.com",
+#}
+#
+#Savon.client(namespaces: namespaces)
+# debug log_level: :debug, log: true, pretty_print_xml: true
+module Sylfy
+    # A module supports as interfaces for web services
+    module Service
+        
+        class SOAPWSDL
+            # Initialize SOAP service
+			#
+			# == Parameters:
+			# wsdl::
+			#   
+			# options::
+			#	
+            def initialize(wsdl, options = {})
+                @options = options
+                @options[:wsdl] = wsdl
+                @options[:log] = false if !@options.has_key?(:log)
+                @options[:pretty_print_xml] = true if @options.has_key?(:log_level) && @options[:log_level] == :debug
+                @client = Savon.client(@options)
+            end
+            
+            # List of methods defined by WSDL
+            def list_methods
+                @client.operations
+            end
+            
+            def method_missing(m, *args, &block)
+                response = @client.call(m, message: args[0])
+                if @options[:log_level] == :debug
+                    puts response.body 
+                    puts response.success?     # => false
+                    puts response.soap_fault?  # => true
+                    puts response.http_error?
+                end
+                
+                if response.body[:"#{m}_response"].has_key?(:"#{m}_return")
+                    result = response.body[:"#{m}_response"][:"#{m}_return"]
+                else
+                    result = response.body[:"#{m}_response"][:return]
+                end
+                
+                if result.class == Hash
+                    result.delete_if {|k, v| k.to_s =~ /^@/}
+                    return result.empty? ? "" : result
+                else
+                    return result
+                end
+            end
+            
+            private :method_missing
+        end
+        
+    end
+end
+
+
+#a = Sylfy::Service::SOAPWSDL.new('http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl')
+#p a.list_methods
+#p a.get_complete_entity(chebiId: '15377').keys #to_xml

data/lib/sylfy/service/unichemrest.rb

@@ -0,0 +1,106 @@
+# 
+# Sylfy library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'open-uri'
+require 'net/http'
+require 'json'
+
+
+module Sylfy
+	
+    module Service
+    
+        module UniChem
+        
+            module REST
+            
+                @@baseuri = "https://www.ebi.ac.uk/unichem/rest"
+                NAMEURIMAPPING = {
+					chembl: "chembl.compound",
+					drugbank: "drugbank",
+					pdb: "pdb",
+					iuphar: "iuphar.ligand",
+					kegg_ligand: "kegg.compound",
+					chebi: "chebi",
+					#emolecules: "",
+					#ibm: "",
+					#atlas: "",
+					#patents: "",
+					#fdasrs: "",
+					#surechem: "",
+					pharmgkb: "pharmgkb.drug",
+					#pubchem_tpharma: "",
+					hmdb: "hmdb",
+					pubchem: "pubchem.compound"
+					#mcule: ""
+				}
+                
+                module_function
+                
+                def perform(input)
+                    
+                    uri = "#{@@baseuri}/#{input}"
+                    
+                    begin
+                        return JSON.parse(open(uri, "content_type" => 'application/json').read().strip())
+                    rescue OpenURI::HTTPError
+                        return JSON.parse("{}")
+                    end
+                end
+                
+                def src_compound_id(src_cpd_id, src_id = 1, to_src_id = nil, all = false)
+                    input = "src_compound_id#{all == true ? "_all" : ''}/#{src_cpd_id}/#{src_id}#{to_src_id != nil ? "/#{to_src_id}" : ""}"
+                    return perform(input)
+                end
+                
+				def src_compound_id_all(src_cpd_id, src_id = 1, to_src_id = nil)
+					return src_compound_id(src_cpd_id, src_id, to_src_id, true)
+				end
+                
+				def mapping(src_id, to_src_id)
+					input = "mapping/#{src_id}/#{to_src_id}"
+					return perform(input)
+				end
+				
+				def inchikey(key, all = false)
+					input = "inchikey#{all == true ? "_all" : ''}/#{key}"
+					return perform(input)
+				end
+				
+				def inchikey_all(key)
+					return inchikey(key, true)
+				end
+				
+				def structure(src_cpd_id, src_id)
+					input = "structure/#{src_cpd_id}/#{src_id}"
+					return perform(input)
+				end
+				
+				def verbose_inchikey(key)
+					input = "verbose_inchikey/#{key}"
+					return perform(input)
+				end
+            end
+            
+            module_function
+                
+			def idbyinchi(inchi)
+				result = []
+				inchi = Rubabel[inchi, :inchi].to_s(:inchikey) if inchi =~ Sylfy::Pattern::INCHI
+				
+				if inchi =~ Sylfy::Pattern::INCHIKEY
+					REST.verbose_inchikey(inchi).each do |entry|
+						if REST::NAMEURIMAPPING.has_key?(entry["name"].to_sym)
+							entry["src_compound_id"].each {|e| result.push("urn:miriam:#{REST::NAMEURIMAPPING[entry["name"].to_sym]}:#{e}")}
+						end
+					end
+				end
+				
+				return result
+			end
+        end
+    end
+end