COEUS 0.0.4

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data/Gemfile

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

data/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2013 Pedro Lopes
+
+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/LICENSE.txt

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+Copyright (c) 2013 Pedro Lopes
+
+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

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+# COEUS gem
+
+A Ruby gem for accessing COEUS API
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'coeus'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install coeus
+
+## Usage
+
+```ruby
+# define COEUS base host address
+COEUS::COEUS.host(new_host)
+``` 
+
+```ruby
+# get triples from COEUS knowledge base (http://bioinformatics.ua.pt/coeus/documentation/#rest)
+# returns JSON array with binded objects
+COEUS::COEUS.triple(subject, predicate, object)
+```
+
+```ruby
+# execute SPARQL query on COEUS host
+# returns RDF::Query::Solution array
+COEUS::COEUS.query(query)
+```

data/Rakefile

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+require "bundler/gem_tasks"

data/coeus.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'coeus/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "COEUS"
+  spec.version       = COEUS::VERSION
+  spec.authors       = ["Pedro Lopes"]
+  spec.email         = ["hello@pedrolopes.net"]
+  spec.description   = %q{COEUS: semantic web application framework}
+  spec.summary       = %q{This. Is. Semantic.}
+  spec.homepage      = "http://bioinformatics.ua.pt/coeus/"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  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", "~> 1.3"
+  spec.add_development_dependency "rake"
+
+  spec.add_dependency "rdf"
+  spec.add_dependency "sparql"
+  spec.add_dependency "json"
+end

data/lib/coeus/version.rb

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+module COEUS
+  VERSION = "0.0.4"
+end

data/lib/coeus.rb

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+require "coeus/version"
+require "open-uri"
+require "json"
+require "rdf"
+require "sparql"
+
+module COEUS
+  class COEUS
+  	@host = 'http://bioinformatics.ua.pt/coeus/'
+  	@key = 'uavr'
+
+  	def self.host(host)
+  		if host.start_with?('http')
+  			@host = host
+  		else
+  			puts 'Invalid host'
+  		end
+  	end
+
+  	def self.open
+  		puts @host
+  	end
+
+  	def self.key(key)
+  		@key = key
+  	end
+
+  	def self.triple(sub, pred, obj)
+  		content = URI.parse(@host + 'api/triple/' + sub + '/' + pred + '/' + obj + '/js').read
+  		return JSON.parse(content)['results']['bindings']
+  	end
+
+  	def self.query(query)
+  		sparql = SPARQL::Client.new(@host + 'sparql')
+  		#queryable = RDF::Repository.load(@host + 'sparql')
+  		#solutions = SPARQL.execute(query, sparql)
+  		#return solutions.to_json
+  		return sparql.query(query)
+  	end
+  end
+end

data/test/test.rb

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+require 'coeus'
+
+class LOL
+#@result = COEUS::COEUS.triple 'coeus:uniprot_P78312', 'coeus:isAssociatedTo', 'obj'
+
+ #@result['results']['bindings'].each do |item|
+ #	puts item['obj']['value']
+ #end
+ @query = "PREFIX coeus: <http://bioinformatics.ua.pt/coeus/resource/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nSELECT * { ?uniprot coeus:hasConcept coeus:concept_UniProt . ?uniprot dc:identifier ?id . ?uniprot dc:title ?name }"
+
+
+ COEUS::COEUS.query(@query).each do |item|
+ 	puts item[:id]
+ end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: COEUS
+version: !ruby/object:Gem::Version
+  version: 0.0.4
+platform: ruby
+authors:
+- Pedro Lopes
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-07-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !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'
+- !ruby/object:Gem::Dependency
+  name: rdf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sparql
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: 'COEUS: semantic web application framework'
+email:
+- hello@pedrolopes.net
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- Gemfile
+- LICENSE
+- LICENSE.txt
+- README.md
+- Rakefile
+- coeus.gemspec
+- lib/coeus.rb
+- lib/coeus/version.rb
+- test/test.rb
+homepage: http://bioinformatics.ua.pt/coeus/
+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: 2.0.3
+signing_key: 
+specification_version: 4
+summary: This. Is. Semantic.
+test_files:
+- test/test.rb