COEUS 0.0.5 → 0.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -0,0 +1,17 @@
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/README.md

@@ -20,17 +20,41 @@ Or install it yourself as:
 
 ```ruby
 # define COEUS base host address
-COEUS::COEUS.host(new_host)
+COEUS::COEUS.host 'http://coeus.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)
-```
+# define COEUS API key
+COEUS::COEUS.key 'api key' 
+``` 
 
 ```ruby
 # execute SPARQL query on COEUS host
 # returns RDF::Query::Solution array
 COEUS::COEUS.query(query)
 ```
+
+```ruby
+# get triples from COEUS knowledge base (http://bioinformatics.ua.pt/coeus/documentation/#rest)
+# returns array with binded objects
+COEUS::COEUS.triple 'subject', 'predicate', 'object'
+```
+
+
+```ruby
+# write triples to COEUS knowledge base (http://bioinformatics.ua.pt/coeus/documentation/#rest)
+# returns true if data written
+COEUS::COEUS.write 'subject','predicate','object'
+```
+
+```ruby
+# updates triple in COEUS knowledge base (http://bioinformatics.ua.pt/coeus/documentation/#rest)
+# returns true if data updated
+COEUS::COEUS.update 'subject','predicate','old object', 'new object'
+```
+
+```ruby
+# delete triple from COEUS knowledge base (http://bioinformatics.ua.pt/coeus/documentation/#rest)
+# returns true if data deleted
+COEUS::COEUS.deleted 'subject','predicate','object'
+```

data/Rakefile

@@ -1 +1,12 @@
 require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new do |t|
+	t.libs << 'test'
+	t.test_files = FileList['test/test*.rb']
+  	t.verbose = true
+end
+
+desc "[COEUS] Run tests"
+
+task :default => :test

data/coeus.gemspec

@@ -9,7 +9,7 @@ Gem::Specification.new do |spec|
   spec.authors       = ["Pedro Lopes"]
   spec.email         = ["pedrolopes@ua.pt"]
   spec.description   = %q{COEUS: semantic web application framework}
-  spec.summary       = %q{This. Is. Semantic.}
+  spec.summary       = %q{Ruby Gem providing direct access to a custom COEUS instance API methods.}
   spec.homepage      = "http://bioinformatics.ua.pt/coeus/"
   spec.license       = "MIT"
 
@@ -24,4 +24,5 @@ Gem::Specification.new do |spec|
   spec.add_dependency "rdf"
   spec.add_dependency "sparql"
   spec.add_dependency "json"
+  spec.add_dependency "rake"
 end

data/lib/coeus.rb

@@ -14,7 +14,7 @@ module COEUS
   	@host = 'http://bioinformatics.ua.pt/coeus/'
 
   	# COEUS API key
-  	@key = 'uavr'
+  	@key = ''
 
   	## 
   	# This method defines the base COEUS host for the next actions
@@ -27,15 +27,25 @@ module COEUS
   	# * http://bioinformatics.ua.pt/coeus/
   	# 
   	def self.host(host)
+  		# verify if valid HTTP URL
   		if host.start_with?('http')
   			@host = host
+
+  			# add final slash (/) if not available
+  			if !@host.end_with?('/')
+  				@host += '/'
+  			end
   		else
-  			puts 'Invalid host'
+  			raise '[COEUS] Invalid host URL'
   		end
   	end
 
-  	def self.open
-  		puts @host
+  	def self.get_host
+  		@host
+  	end
+
+  	def self.print
+  		puts "[COEUS] instance details\n\t- Host: #{@host}\n\t- API key: #{@key}"
   	end
 
   	## 
@@ -52,6 +62,10 @@ module COEUS
   		@key = key
   	end
 
+  	def self.get_key
+  		@key
+  	end
+
   	## 
   	# This method uses COEUS API to get match triples based on provided parameters
   	#
@@ -60,9 +74,6 @@ module COEUS
   	# * +sub+ - the triple set subject
   	# * +pred+ - the triple set predicate
   	# * +obj+ - the triple set object
-  	#
-  	# ==== Default
-  	# * http://bioinformatics.ua.pt/coeus/
   	# 
   	def self.triple(sub, pred, obj)
   		content = URI.parse(@host + 'api/triple/' + sub + '/' + pred + '/' + obj + '/js').read
@@ -81,5 +92,79 @@ module COEUS
   		sparql = SPARQL::Client.new(@host + 'sparql')
   		return sparql.query(query)
   	end
+
+	## 
+  	# This method uses COEUS API to get write new triples based on provided parameters.
+  	# *Note:* Requires that the API key is previously defined
+  	#
+  	# ==== Parameters
+  	#
+  	# * +sub+ - the new triple subject
+  	# * +pred+ - the new triple predicate
+  	# * +obj+ - the new riple object
+  	# 
+  	def self.write(sub, pred, obj)
+  		if @key == ''
+  			raise '[COEUS] undefined API key'
+  		else
+	  		content = URI.parse(@host + 'api/' + @key + '/write/' + sub + '/' + pred + '/' + obj).read
+	  		result = JSON.parse(content)
+	  		if result['status'] != 100
+	  			raise '[COEUS] unable to store triple: ' + result['message']
+	  		else
+	  			return true
+	  		end
+	  	end
+  	end
+
+  	## 
+  	# This method uses COEUS API to get update existing triples based on provided parameters.
+  	# *Note:* Requires that the API key is previously defined
+  	#
+  	# ==== Parameters
+  	#
+  	# * +sub+ - the triple subject
+  	# * +pred+ - the triple predicate
+  	# * +old_obj+ - the old triple object
+  	# * +new_obj+ - the new triple object
+  	# 
+  	def self.update(sub, pred, old_obj, new_obj)
+  		if @key == ''
+  			raise '[COEUS] undefined API key'
+  		else
+	  		content = URI.parse(@host + 'api/' + @key + '/update/' + sub + '/' + pred + '/' + old_obj + ',' + new_obj).read
+	  		result = JSON.parse(content)
+	  		if result['status'] != 100
+	  			raise '[COEUS] unable to update triple: ' + result['message']
+	  		else
+	  			return true
+	  		end
+	  	end
+  	end
+
+	## 
+  	# This method uses COEUS API to get delete triples based on provided parameters.
+  	# *Note:* Requires that the API key is previously defined
+  	#
+  	# ==== Parameters
+  	#
+  	# * +sub+ - the triple subject to delete
+  	# * +pred+ - the triple predicate to delete
+  	# * +obj+ - the riple object to delete
+  	# 
+  	def self.delete(sub, pred, obj)
+  		if @key == ''
+  			raise '[COEUS] undefined API key'
+  		else
+	  		content = URI.parse(@host + 'api/' + @key + '/delete/' + sub + '/' + pred + '/' + obj).read
+	  		result = JSON.parse(content)
+	  		if result['status'] != 100
+	  			raise '[COEUS] unable to delete triple: ' + result['message']
+	  		else
+	  			return true
+	  		end
+	  	end
+  	end
+
   end
 end

data/lib/coeus/version.rb

@@ -1,4 +1,4 @@
 module COEUS
 	# COEUS gem version info
-	VERSION = "0.0.5"
+	VERSION = "0.1"
 end

data/test/test_coeus.rb

@@ -0,0 +1,65 @@
+require 'test/unit'
+require "open-uri"
+require 'coeus'
+
+class Test_COEUS < Test::Unit::TestCase
+	def test_host
+		COEUS::COEUS.host('http://bioinformatics.ua.pt/diseasecard')
+		assert_equal 'http://bioinformatics.ua.pt/diseasecard/', COEUS::COEUS.get_host
+	end
+
+	def test_key
+		COEUS::COEUS.key('12345')
+		assert_equal '12345', COEUS::COEUS.get_key
+	end
+
+	def test_sparql
+		@query = "PREFIX coeus: <http://bioinformatics.ua.pt/coeus/resource/>\nSELECT COUNT(DISTINCT ?tag) { ?tag coeus:hasConcept coeus:concept_UniProt}"
+		assert_equal COEUS::COEUS.query(@query).size, 1
+	end
+
+	def test_triple
+		@result = COEUS::COEUS.triple 'coeus:concept_UniProt', 'dc:title', 'obj'
+		assert_instance_of Array, @result
+	end
+
+	def test_write
+		COEUS::COEUS.key 'uavr'
+		@result = COEUS::COEUS.write 'coeus:gemx','dc:title','gemx'
+		assert @result
+	end
+
+	def test_update
+		COEUS::COEUS.key 'uavr'
+		@result = COEUS::COEUS.update 'coeus:gemx','dc:title','gemx','gemy'
+		assert @result
+	end
+
+	def test_delete
+		COEUS::COEUS.key 'uavr'
+		@result = COEUS::COEUS.delete 'coeus:gemx','dc:title','gemy'
+		assert @result
+	end
+
+	def test_all
+		# set API key
+		COEUS::COEUS.key 'uavr'
+
+		# write new triple
+		assert COEUS::COEUS.write('coeus:gem_x','dc:title','gem_x')
+
+		# check added triple output
+		@res = COEUS::COEUS.triple 'coeus:gem_x', 'dc:title', 'obj'
+		assert_equal @result[0]["obj"]["value"], "gem_x"
+
+		# update triple content
+		assert COEUS::COEUS.update('coeus:gem_x','dc:title','gem_x', 'coeus-gem')
+
+		# check updated triple content
+		@res = COEUS::COEUS.triple 'coeus:gem_x', 'dc:title', 'obj'
+		assert_equal @result[0]["obj"]["value"], "coeus-gem"
+
+		# delete triple
+		assert COEUS::COEUS.delete('coeus:gem_x','dc:title','coeus-gem')
+	end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: COEUS
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: '0.1'
 platform: ruby
 authors:
 - Pedro Lopes
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-17 00:00:00.000000000 Z
+date: 2013-07-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -80,6 +80,20 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  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:
 - pedrolopes@ua.pt
@@ -87,13 +101,14 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- .gitignore
 - Gemfile
 - README.md
 - Rakefile
 - coeus.gemspec
 - lib/coeus.rb
 - lib/coeus/version.rb
-- test/test.rb
+- test/test_coeus.rb
 homepage: http://bioinformatics.ua.pt/coeus/
 licenses:
 - MIT
@@ -117,6 +132,6 @@ rubyforge_project:
 rubygems_version: 2.0.3
 signing_key: 
 specification_version: 4
-summary: This. Is. Semantic.
+summary: Ruby Gem providing direct access to a custom COEUS instance API methods.
 test_files:
-- test/test.rb
+- test/test_coeus.rb

data/test/test.rb

@@ -1,15 +0,0 @@
-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