myGrid-taverna-scufl 0.6.0

data/test/fixtures/animal.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" version="0.2" log="0">
+  <s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:6ebc9ec6-1045-459d-a26c-74e4efe2d6f8" author="" title="animal" />
+  <s:processor name="AnimalFactory" boring="true">
+    <s:stringconstant>frog</s:stringconstant>
+  </s:processor>
+  <s:link source="AnimalFactory:value" sink="animal" />
+  <s:sink name="animal" />
+</s:scufl>
+

data/test/fixtures/colouranimal.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" version="0.2" log="0">
+  <s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:a378c99c-b85e-46cd-91be-47ac93cde18c" author="" title="animal" />
+  <s:processor name="colour_the_animal">
+    <s:local>org.embl.ebi.escience.scuflworkers.java.StringConcat</s:local>
+  </s:processor>
+  <s:link source="animal" sink="colour_the_animal:string2" />
+  <s:link source="colour" sink="colour_the_animal:string1" />
+  <s:link source="colour_the_animal:output" sink="coulouredAnimal" />
+  <s:source name="animal" />
+  <s:source name="colour" />
+  <s:sink name="coulouredAnimal" />
+</s:scufl>
+

data/test/tc_client.rb

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+$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
+
+require 'test/unit'
+require 'enactor/client'
+require 'document/data'
+
+class TcClient < Test::Unit::TestCase
+
+	FIXTURES = File.join(File.dirname(__FILE__), "fixtures")
+	
+	TEST_SERVER="http://rpc269.cs.man.ac.uk:8180/remotetaverna/v1/"
+	TEST_USER="snake"
+	TEST_PW=IO.read("#{FIXTURES}/password.txt").strip
+	
+	# Test workflows
+	ANIMAL_WF=IO.read("#{FIXTURES}/animal.xml")
+	COLOUR_ANIMAL_WF=IO.read("#{FIXTURES}/colouranimal.xml")
+		
+    def setup
+    	@service = Enactor::Client.new(TEST_SERVER, TEST_USER, TEST_PW)
+    end
+	
+	def test_connect
+		capabilities_doc = @service.get_capabilities_doc()
+        #users = capabilities.elements["{http://taverna.sf.net/service}users"]
+        users = capabilities_doc.root.elements["users"]
+        users_url = users.attributes.get_attribute_ns('http://www.w3.org/1999/xlink', 'href').value
+        assert_equal(TEST_SERVER  + "users", users_url)
+	end
+    
+    def test_get_user_url
+        user_url = @service.get_user_url()
+        assert_equal(TEST_SERVER + "users/" + TEST_USER, user_url)
+    end
+    
+    def test_get_user_collection_url
+        workflow_url = @service.get_user_collection_url("workflows")
+        assert_equal(TEST_SERVER + "users/" + TEST_USER + "/workflows", workflow_url)
+        job_url = @service.get_user_collection_url("jobs")
+        assert_equal(TEST_SERVER + "users/" + TEST_USER + "/jobs", job_url)
+        data_url = @service.get_user_collection_url("datas")
+        assert_equal(TEST_SERVER + "users/" + TEST_USER + "/data", data_url)
+    end
+    
+    def test_upload_workflow
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        prefix = TEST_SERVER + "workflows/"
+        assert(workflow_url.index(prefix) == 0)
+    end
+        
+	def test_workflow_exists
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+		assert(@service.workflow_exists?(workflow_url))
+		assert(!@service.workflow_exists?(workflow_url.chop))
+	end
+	
+	def test_service_valid
+		assert(@service.service_valid?)
+		assert(!Enactor::Client.new(TEST_SERVER, TEST_USER, TEST_PW.chop).service_valid?)
+	end
+	
+    def test_create_job
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        job_doc = @service.create_job_doc(workflow_url)
+        #workflow_element = job_doc.elements["{http://taverna.sf.net/service}workflow"]
+        workflow_element = job_doc.root.elements['workflow']
+        assert_equal(workflow_url, workflow_element.attributes.get_attribute_ns('http://www.w3.org/1999/xlink', 'href').value)
+    end
+    
+    def test_submit_job
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        job_url = @service.submit_job(workflow_url)
+        prefix = TEST_SERVER + "jobs/"
+        assert(job_url.index(prefix) == 0)
+    end 
+    
+    def test_create_data
+        inputs = {}
+        inputs['colour'] = Document::Data.new('red')
+        inputs['animal'] = Document::Data.new('snake')
+        data_document = @service.create_data_doc(inputs)
+        parsed = @service.parse_data_doc(data_document)
+        assert_equal(inputs, parsed)
+    end
+    
+    def test_upload_data
+        inputs = {}
+        inputs["colour"] = Document::Data.new("red")
+        inputs["animal"] = Document::Data.new("snake")
+        data_url = @service.upload_data(inputs)
+        prefix = TEST_SERVER + "data/"
+        assert(data_url.index(prefix) == 0)
+    end
+	
+    def test_submit_job_with_data
+        inputs = {}
+        inputs["colour"] = Document::Data.new("red")
+        inputs["animal"] = Document::Data.new("snake")
+        workflow_url = @service.upload_workflow(COLOUR_ANIMAL_WF)
+        data_url = @service.upload_data(inputs)
+        job_url = @service.submit_job(workflow_url, data_url)
+    end
+	
+    def test_get_job_status
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        job_url = @service.submit_job(workflow_url)
+        status = @service.get_job_status(job_url)
+        assert(Enactor::Status.valid?(status))
+    end
+        
+    def test_get_job_created_date
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        job_url = @service.submit_job(workflow_url)
+		time = @service.get_job_created_date(job_url)
+		assert(time.kind_of?(DateTime))
+    end
+        
+    def test_get_job_modified_date
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        job_url = @service.submit_job(workflow_url)
+		time = @service.get_job_modified_date(job_url)
+		assert(time.kind_of?(DateTime))
+    end
+        
+    def test_finished
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        job_url = @service.submit_job(workflow_url)
+        # Assuming our server is not VERY quick
+        assert(!@service.finished?(job_url))
+    end
+                         
+    def test_job_outputs_size
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        job_url = @service.submit_job(workflow_url)
+        @service.wait_for_job(job_url, 30)
+		assert_equal(481, @service.get_job_outputs_size(job_url))
+    end
+        
+    def test_wait_for_job
+        workflow_url = @service.upload_workflow(ANIMAL_WF)
+        job_url = @service.submit_job(workflow_url)
+        now = Time.now
+        timeout = 1
+        status = @service.wait_for_job(job_url, timeout)
+        after = Time.now
+
+        # Should be at least some milliseconds longer than the timeout
+        assert(after - now > timeout)
+        assert(!@service.finished?(job_url))
+    end
+        
+    def test_execute
+        # Note: This test might take a minute or so to complete
+        results = @service.execute_sync(ANIMAL_WF)
+        assert_equal(1, results.length)
+        assert_equal("frog", results["animal"].value)
+    end
+        
+    def test_execute_with_data
+        # Note: This test might take a minute or so to complete
+        inputs = {}
+        inputs["colour"] = Document::Data.new("red")
+        inputs["animal"] = Document::Data.new("snake")
+        workflow_url = @service.upload_workflow(COLOUR_ANIMAL_WF)
+        results = @service.execute_sync(nil, workflow_url, inputs)
+
+        assert_equal(1, results.length)
+        assert_equal("redsnake", results["coulouredAnimal"].value)
+    end
+        
+    def test_execute_with_multiple_data
+        # Note: This test might take a minute or so to complete
+        inputs = {}
+        inputs["colour"] = Document::Data.new(["red", "green"])
+        inputs["animal"] = Document::Data.new(["rabbit", "mouse", "cow"])
+        workflow_url = @service.upload_workflow(COLOUR_ANIMAL_WF)
+        results = @service.execute_sync(nil, workflow_url, inputs)
+
+        assert_equal(1, results.length)
+        animals = results["coulouredAnimal"].value
+
+		assert_equal(2, animals.length)
+		animals = animals[0] + animals[1]
+		assert_equal(6, animals.length)
+
+        assert(animals.include?("redmouse"))
+        assert(animals.include?("greenrabbit"))
+        assert(!animals.include?("redsnake"))
+    end
+	
+end

data/test/ts_taverna.rb

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+$:.unshift File.join(File.dirname(__FILE__), ".")
+
+require 'test/unit' 
+require 'tc_client' 

metadata

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+--- !ruby/object:Gem::Specification 
+name: myGrid-taverna-scufl
+version: !ruby/object:Gem::Version 
+  version: 0.6.0
+platform: ruby
+authors: 
+- David Withers
+- Emmanuel Tagarira
+autorequire: baclava, client, document, scufl
+bindir: bin
+cert_chain: 
+date: 2009-08-18 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rdoc
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.4.3
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: darkfish-rdoc
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.1.5
+    version: 
+description: This a gem developed by myGrid for the purpose of interacting with Taverna 1 workflows.  An example use would be the image genaration for the model representing Taverna 1 workflows as used in myExperiment.
+email: david.withers@manchester.ac.uk
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README
+- LICENCE
+files: 
+- test/fixtures
+- test/fixtures/animal.xml
+- test/fixtures/colouranimal.xml
+- test/tc_client.rb
+- test/ts_taverna.rb
+- lib/baclava
+- lib/baclava/reader.rb
+- lib/baclava/writer.rb
+- lib/document
+- lib/document/data.rb
+- lib/document/report.rb
+- lib/enactor
+- lib/enactor/client.rb
+- lib/scufl
+- lib/scufl/dot.rb
+- lib/scufl/model.rb
+- lib/scufl/parser.rb
+- README
+- LICENCE
+has_rdoc: true
+homepage: http://www.mygrid.org.uk/
+licenses: 
+post_install_message: 
+rdoc_options: 
+- -N
+- --tab-width=2
+- --main=README
+- --exclude='scufl.gemspec|test'
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: 1.0.1
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 1
+summary: Support for interacting with the Taverna workflow system (Scufl).
+test_files: 
+- test/ts_taverna.rb