wf4ever-transformation-client 0.3.1 → 0.4.0

checksums.yaml

@@ -0,0 +1,15 @@
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data/Gemfile

@@ -7,6 +7,6 @@ source "http://rubygems.org"
 # Include everything needed to run rake, tests, features, etc.
 group :development do
   gem "rdoc", "~> 3.12"
-  gem "bundler", "~> 1.1.5"
+  gem "bundler", "~> 1.1"
   gem "jeweler", "~> 1.8.4"
 end

data/README.rdoc

@@ -1,20 +1,39 @@
 = transformation-client
 
-== Usage ==
+This is a Ruby client library for submitting jobs to the
+Wf4Ever wf-ro transformation service - for details, see 
+http://www.wf4ever-project.org/wiki/display/docs/Wf-RO+transformation+service+API
+
+== Usage
 Require the gem
   require 'wf4ever/transformation-client'
 
 To create a job:
-  uri = Wf4Ever::TransformationClient.create_job(service-uri, resource-uri, format-uri, ro-uri, oauth-token)
+  service = "http://example.com/wf-ro/jobs"
+  resource = "http://example.net/workflow.t2flow"
+  format = "application/vnd.taverna.t2flow+xml"
+  ro = "http://example.com/RODL/RO/myResearch/"
+  token = "e5e02dd4-9e29-43f0-890c-729d66c46a9b"
+
+  job_uri = Wf4Ever::TransformationClient.create_job(service, resource, format, ro, token)
+
+You can optionally provide a list of additional resources to extract to
+which folders in the RO.
+
+  extract = { :nested => "http://example.com/RODL/RO/myResearch/folder1" } 
+  job_uri = Wf4Ever::TransformationClient.create_job(service, resource, format, ro, token, extract)
 
 To check the status of a job
-  status = Wf4Ever::TransformationClient.check_job(uri)["status"]
+  status = Wf4Ever::TransformationClient.check_job(job_uri)["status"]
 
 To cancel a job
-  Wf4Ever::TransformationClient.cancel_job(uri)
+  Wf4Ever::TransformationClient.cancel_job(job_uri)
+
 
 == Copyright
 
-Copyright (c) 2012 Finn Bacall. See LICENSE.txt for
-further details.
+Copyright (c) 2012-2013 University of Manchester. 
+
+This software is freely available under the MIT License. See LICENSE.txt
+for further details.
 

data/Rakefile

@@ -15,12 +15,12 @@ require 'jeweler'
 Jeweler::Tasks.new do |gem|
   # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
   gem.name = "wf4ever-transformation-client"
-  gem.homepage = "http://github.com/myGrid/transformation-client"
+  gem.homepage = "http://github.com/myExperiment/transformation-client"
   gem.license = "MIT"
   gem.summary = "Client to interact with Wf4ever's RO Transformation Service"
   gem.description = "Client to interact with Wf4ever's RO Transformation Service"
-  gem.email = "finn.bacall@cs.man.ac.uk"
-  gem.authors = ["Finn Bacall"]
+  gem.email = "bugs@myexperiment.org"
+  gem.authors = ["Finn Bacall", "Stian Soiland-Reyes"]
   # dependencies defined in Gemfile
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.3.1
+0.4.0

data/lib/wf4ever/transformation-client.rb

@@ -5,18 +5,51 @@ module Wf4Ever
   class TransformationClient
 
     ##
-    # Creates a transformation job and returns its URI.
-    def self.create_job(uri, resource, format, ro, token)
+    # Create a transformation job and returns its URI, which can be
+    # used with check_job() and cancel_job()
+    #
+    # uri -- The URI for the wf-ro service endpoint, e.g.
+    #   "http://example.com/wf-ro/jobs"
+    # resource - The URI for the workflow resource to transform, e.g.
+    #   "http://www.example.net/workflow.t2flow"
+    # format - the media type of the resource, e.g.
+    #   "application/vnd.taverna.t2flow+xml"
+    # ro - the URI for the research object within an RODL service,
+    #   where the transformed and extracted resources are to be uploaded
+    # token - token for authenticating access to the RODL
+    # extract -
+    #   (optional) hash of folders where to extract additional
+    #   resources. The main workflow is always extracted, but will
+    #   only be placed into a folder if it is given in the hash. Other
+    #   resource types are only extracted if listed in the map. 
+    #
+    #   The extract keys should be one of:
+    #     - :main -- transformed workflow 
+    #     - :nested -- nested workflows
+    #     - :scripts -- embedded scripts (e.g. beanshell, R)
+    #     - :services -- external services (e.g. WSDL, REST)
+    #   
+    #   The extract values are URIs to RODL folders within the RO where to
+    #   extract the resource. A value using the keyword :ro means to
+    #   extract the particular resource without aggregating it in any 
+    #   particular folder.
+    def self.create_job(uri, resource, format, ro, token, extract={:main=>:ro})
       uri = URI(uri)
       job_uri = nil
+      ## Replace :ro with the ro URI as per wf-ro REST API
+      # We'll do this in a new hash to not modify our incoming hash
+      # TODO: Avoid Perl-like syntax below..
+      extract = extract.each_with_object({}) { |(k,v), h|  h[k] = v==:ro ? ro : v } 
+
       Net::HTTP.start(uri.host, uri.port || 80) do |http|
         body = {
           "resource" => resource,
           "format" => format,
           "ro" => ro,
-          "token" => token
+          "token" => token,
+          "extract" => extract
         }.to_json
-
+        
         headers = {"content-type" => "application/json"}
 
         response = http.post(uri.request_uri, body, headers)
@@ -31,11 +64,14 @@ module Wf4Ever
     end
 
     ##
-    # Returns a hash containing: 
+    # Check wf-ro transformation job status.
+    #
+    # Return a hash containing: 
     # ["resource"]  the resource being transformed
     # ["format"]    the content type of the resource
     # ["ro"]        the URI of the RO being created
     # ["status"]    the status of the transformation job  
+    # ["extract"]   the resource type to extract, to which folder
     def self.check_job(uri)
       uri = URI(uri)
       Net::HTTP.start(uri.host, uri.port || 80) do |http|
@@ -52,7 +88,7 @@ module Wf4Ever
     end
 
     ##
-    # Cancels job and returns true if it succeeds.
+    # Cancel wf-ro transformation job and returns true if it succeeds.
     def self.cancel_job(uri)
       uri = URI(uri)
       Net::HTTP.start(uri.host, uri.port || 80) do |http|

data/test/test_transformation-client.rb

@@ -9,8 +9,42 @@ class TestTransformationClient < Test::Unit::TestCase
   RO = "http://sandbox.wf4ever-project.org/rodl/ROs/FinnsTest/"
 
   def test_can_create
-    uri = Wf4Ever::TransformationClient.create_job(SERVICE_URI, RESOURCE, T2FLOW_FORMAT, RO, OAUTH_TOKEN)
-    assert_not_nil uri
+    @uri = Wf4Ever::TransformationClient.create_job(SERVICE_URI, RESOURCE, T2FLOW_FORMAT, RO, OAUTH_TOKEN)
+    assert_not_nil @uri
+    status = Wf4Ever::TransformationClient.check_job(@uri)
+    #puts status
+    assert_equal(RESOURCE, status["resource"])
+    assert_equal(T2FLOW_FORMAT, status["format"])
+    assert_equal(RO, status["ro"])
+    # :ro default should become 'main'
+    assert_equal(RO, status["extract"]["main"])
+    ## The remaining folders should not be listed
+    assert_nil(status["extract"]["nested"])
+    assert_nil(status["extract"]["scripts"])
+    assert_nil(status["extract"]["services"])
+  end
+
+  def setup
+      @uri = nil
+  end
+
+  def teardown
+    Wf4Ever::TransformationClient.cancel_job(@uri) if @uri
+  end
+
+  def test_with_extract
+    extract = {:nested => RO + "folderNested", :scripts => :ro, :main => RO + "folderMain"} 
+    @uri = Wf4Ever::TransformationClient.create_job(SERVICE_URI, RESOURCE, T2FLOW_FORMAT, RO, OAUTH_TOKEN, extract)
+    assert_not_nil @uri
+    status = Wf4Ever::TransformationClient.check_job(@uri)
+#    puts status
+    assert_equal(RESOURCE, status["resource"])
+    assert_equal(T2FLOW_FORMAT, status["format"])
+    assert_equal(RO, status["ro"])
+    assert_equal(RO + "folderMain", status["extract"]["main"])
+    assert_equal(RO + "folderNested", status["extract"]["nested"])
+    assert_equal(RO, status["extract"]["scripts"])
+    assert_nil(status["extract"]["services"])
   end
 
 end

data/wf4ever-transformation-client.gemspec

@@ -2,16 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: wf4ever-transformation-client 0.4.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "wf4ever-transformation-client"
-  s.version = "0.3.1"
+  s.version = "0.4.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Finn Bacall"]
-  s.date = "2012-10-05"
+  s.authors = ["Finn Bacall", "Stian Soiland-Reyes"]
+  s.date = "2013-12-20"
   s.description = "Client to interact with Wf4ever's RO Transformation Service"
-  s.email = "finn.bacall@cs.man.ac.uk"
+  s.email = "bugs@myexperiment.org"
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -29,27 +30,27 @@ Gem::Specification.new do |s|
     "test/test_transformation-client.rb",
     "wf4ever-transformation-client.gemspec"
   ]
-  s.homepage = "http://github.com/myGrid/transformation-client"
+  s.homepage = "http://github.com/myExperiment/transformation-client"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.10"
+  s.rubygems_version = "2.1.11"
   s.summary = "Client to interact with Wf4ever's RO Transformation Service"
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.1.5"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.1"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
     else
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<bundler>, ["~> 1.1.5"])
+      s.add_dependency(%q<bundler>, ["~> 1.1"])
       s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
     end
   else
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<bundler>, ["~> 1.1.5"])
+    s.add_dependency(%q<bundler>, ["~> 1.1"])
     s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
   end
 end

metadata

@@ -1,51 +1,60 @@
 --- !ruby/object:Gem::Specification
 name: wf4ever-transformation-client
 version: !ruby/object:Gem::Version
-  version: 0.3.1
-  prerelease: 
+  version: 0.4.0
 platform: ruby
 authors:
 - Finn Bacall
+- Stian Soiland-Reyes
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-10-05 00:00:00.000000000 Z
+date: 2013-12-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &19580800 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *19580800
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &19580280 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.5
+        version: '1.1'
   type: :development
   prerelease: false
-  version_requirements: *19580280
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.1'
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &19579740 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *19579740
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
 description: Client to interact with Wf4ever's RO Transformation Service
-email: finn.bacall@cs.man.ac.uk
+email: bugs@myexperiment.org
 executables: []
 extensions: []
 extra_rdoc_files:
@@ -63,32 +72,28 @@ files:
 - test/helper.rb
 - test/test_transformation-client.rb
 - wf4ever-transformation-client.gemspec
-homepage: http://github.com/myGrid/transformation-client
+homepage: http://github.com/myExperiment/transformation-client
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 4569034392740922883
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 2.1.11
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Client to interact with Wf4ever's RO Transformation Service
 test_files: []