myexperiment-rest 0.2.8 → 0.3.0

data/lib/myexperiment-rest/workflow.rb

@@ -0,0 +1,145 @@
+require 'libxml'
+
+module MyExperimentREST
+
+  #
+  # Connects to myExperiment REST API and creates a _MyExperimentWorkflow_ object.
+  #
+  class Workflow
+
+    # Returns a _MyExperimentWorkflow_ object given a URI of the workflow in the repository as a String.
+    def self.from_uri(uri)
+
+      workflow_id = ''
+      workflow_version = ''
+
+      # Get workflow id - will match both workflow/74 and workflows.xml?id=74
+      uri_id = uri.match(/workflow.*[\/?](id=)?(\d+)/)
+      if uri_id != nil
+        workflow_id = uri_id[2]
+      else
+        raise "Could not match workflow id."
+      end
+
+      # Get workflow version if it exists
+      uri_version = uri.match(/version=(\d+)/)
+      if uri_version != nil
+        workflow_version = uri_version[1]
+      end
+
+      # Get workflow resource information 
+      xml = MyExperimentREST.get_myexperiment_data(Urls::WORKFLOW_URL, :id => workflow_id, :version => workflow_version)
+      
+      MyExperimentWorkflow.parse(xml)
+    end
+
+
+    # Returns a _MyExperimentWorkflow_ object given a myExperiment id and version for that workflow.
+    def self.from_id_and_version(id, version='')
+
+      # Get workflow resource information
+      xml = MyExperimentREST.get_myexperiment_data(Urls::WORKFLOW_URL, :id => id, :version => version)
+
+      MyExperimentWorkflow.parse(xml)
+    end
+
+
+  end  # class Workflow
+
+
+
+  #
+  # Contains all available information about a workflow: _xml_uri_,
+  # _title_, _description_,_inputs_, _outputs_ and _uploader_uri_. The _xml_uri_
+  # specifies the XML description on myExperiment and not the XML of the workflow
+  # itself.
+  #
+  class MyExperimentWorkflow
+    
+    attr_reader(:xml_uri, :title, :description, :inputs, :outputs, :uploader_uri)
+
+    def initialize(attributes)
+      @xml_uri = attributes[:xml_uri]
+      @title = attributes[:title]
+      @description = attributes[:description]
+      @inputs = attributes[:inputs]
+      @outputs = attributes[:outputs]
+      @uploader_uri = attributes[:uploader_uri]
+    end
+
+    # Parse workflow information XML and instantiate a _MyExperimentWorkflow_ object
+    def self.parse(xml)
+
+      wkf_inputs = []
+      wkf_outputs = []
+
+      doc = LibXML::XML::Document.string(xml)
+
+      doc.find("//workflow/components/dataflows/dataflow[@role='top']/sources/source").each do |element|
+        wkf_inputs << MyExperimentIOData.from_xml(element)
+      end
+
+      doc.find("//workflow/components/dataflows/dataflow[@role='top']/sinks/sink").each do |element|
+        wkf_outputs << MyExperimentIOData.from_xml(element)
+      end
+
+
+      new(:xml_uri => doc.find_first("/workflow/content-uri").content,
+          :title => doc.find_first("/workflow/title").content,
+          :description => doc.find_first("/workflow/description").content,
+          :inputs => wkf_inputs,
+          :outputs => wkf_outputs,
+          :uploader_uri => doc.find_first("/workflow/uploader").attributes['uri'])
+
+    end
+
+  end
+
+
+  #
+  # Contains all available information about an input or output: name, descriptions
+  # and examples. The last two are lists.
+  #--
+  # Currently both inputs and outputs contain the same information. If that
+  # changes we can subclass this one.
+  #
+  class MyExperimentIOData
+    attr_reader(:name, :descriptions, :examples)
+
+    def initialize(attributes)
+      @name = attributes[:name]
+      @descriptions = attributes[:descriptions]
+      @examples = attributes[:examples]
+    end
+
+    def self.from_xml(xml_node)
+      name = ''
+      descriptions = []
+      examples = []
+
+      xml_node.each_element do |n|
+        if n.name.eql? "name"
+          name = n.children[0].to_s
+        elsif n.name.eql? "descriptions"
+          n.each_element do |d|
+            descriptions << d.children[0].to_s
+          end if n.children?
+        elsif n.name.eql? "examples"
+          n.each_element do |e|
+            examples << e.children[0].to_s
+          end if n.children?
+        end
+      end
+
+
+      new(
+        :name => name,
+        :descriptions => descriptions,
+        :examples => examples)
+
+    end
+
+  end  # class MyExperimentIOData
+
+end  # module
+

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: myexperiment-rest
 version: !ruby/object:Gem::Version 
-  hash: 7
+  hash: 19
   prerelease: 
   segments: 
   - 0
-  - 2
-  - 8
-  version: 0.2.8
+  - 3
+  - 0
+  version: 0.3.0
 platform: ruby
 authors: 
 - Konstantinos Karasavvas
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-09-19 00:00:00 Z
+date: 2011-09-28 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: rest-client
@@ -41,12 +41,12 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        hash: 5
+        hash: 29
         segments: 
         - 2
         - 0
-        - 5
-        version: 2.0.5
+        - 9
+        version: 2.0.9
   type: :runtime
   version_requirements: *id002
 description: This is a simple library to access data on myExperiment via its REST API. Currently supports a subset of the workflow information available.
@@ -66,7 +66,9 @@ files:
 - Rakefile
 - bin/get_workflow_data.rb
 - lib/myexperiment-rest.rb
-- lib/myexperiment-rest/myexperiment_rest.rb
+- lib/myexperiment-rest/workflow.rb
+- lib/myexperiment-rest/user.rb
+- lib/myexperiment-rest/constants.rb
 - doc/rdoc/rdoc.css
 - doc/rdoc/LICENSE.html
 - doc/rdoc/index.html
@@ -76,7 +78,9 @@ files:
 - doc/rdoc/js/quicksearch.js
 - doc/rdoc/MyExperimentREST.html
 - doc/rdoc/README.html
-- doc/rdoc/lib/myexperiment-rest/myexperiment_rest_rb.html
+- doc/rdoc/lib/myexperiment-rest/constants_rb.html
+- doc/rdoc/lib/myexperiment-rest/user_rb.html
+- doc/rdoc/lib/myexperiment-rest/workflow_rb.html
 - doc/rdoc/lib/myexperiment-rest_rb.html
 - doc/rdoc/created.rid
 - doc/rdoc/CHANGES.html
@@ -100,10 +104,12 @@ files:
 - doc/rdoc/images/page_white_width.png
 - doc/rdoc/images/package.png
 - doc/rdoc/images/plugin.png
-- doc/rdoc/MyExperimentREST/TavernaUser.html
-- doc/rdoc/MyExperimentREST/TavernaIOData.html
-- doc/rdoc/MyExperimentREST/Workflows.html
-- doc/rdoc/MyExperimentREST/TavernaWorkflow.html
+- doc/rdoc/MyExperimentREST/User.html
+- doc/rdoc/MyExperimentREST/Urls.html
+- doc/rdoc/MyExperimentREST/MyExperimentWorkflow.html
+- doc/rdoc/MyExperimentREST/MyExperimentUser.html
+- doc/rdoc/MyExperimentREST/MyExperimentIOData.html
+- doc/rdoc/MyExperimentREST/Workflow.html
 homepage: 
 licenses: []
 
@@ -136,6 +142,6 @@ rubyforge_project:
 rubygems_version: 1.7.2
 signing_key: 
 specification_version: 3
-summary: This is a simple library to access data on myExperiment via its REST API. Currently supports a subset of the workflow information available.
+summary: This is a simple library to access data on myExperiment via its REST API.
 test_files: []
 

data/lib/myexperiment-rest/myexperiment_rest.rb

@@ -1,190 +0,0 @@
-require 'rubygems'
-require 'rest_client'
-require 'open-uri'
-require 'libxml'
-
-module MyExperimentREST
-
-  #
-  # Connects to myExperiment REST API and creates a _TavernaWorkflow_ object.
-  #
-  class Workflows
-    include LibXML
-
-    attr_reader(:uri)
-
-    #def initialize
-    #end
-
-    # Requires the URI of the workflow in the repository as a String.
-    def read(uri)
-
-      workflow_id = ''
-      workflow_version = ''
-
-      # Get workflow id
-      uri_id = uri.match(/workflows\/(\d+)/)
-      if uri_id != nil
-        workflow_id = uri_id[1]
-      else
-        raise "Could not match workflow id."
-      end
-
-      # Get workflow version if it exists
-      uri_version = uri.match(/version=(\d+)/)
-      if uri_version != nil
-        workflow_version = uri_version[1]
-      end
-
-      # Get workflow resource information -- if version is empty it returns the current version
-      response = RestClient.get('http://www.myexperiment.org/workflow.xml', {:params => {'id' => "#{workflow_id}", 
-                                                                                         'version' => "#{workflow_version}",
-                                                                                         'elements' => 'title,description,content-uri,components,uploader'} } )
-
-      populate_workflow(response)
-    end
-
-
-    private
-
-    # Acquire data from XML response and instantiate a _Taverna_Workflow_ object
-    #--
-    # TODO: refactor so that each (logical) workflow element is an object with
-    # its own read from_xml method...
-    def populate_workflow(response)
-      doc = XML::Document.string(response)
-      wkf_xml_uri = doc.find_first("/workflow/content-uri").content
-      wkf_title = doc.find_first("/workflow/title").content
-      wkf_descr = doc.find_first("/workflow/description").content
-      wkf_inputs = get_IOData(doc, "source")
-      wkf_outputs = get_IOData(doc, "sink")
-      wkf_user = get_user(doc.find_first("/workflow/uploader").attributes['uri'])
-
-      TavernaWorkflow.new(TavernaWorkflow::MY_EXPERIMENT, wkf_xml_uri, wkf_title, wkf_descr, wkf_inputs, wkf_outputs, wkf_user)
-
-    end
-
-
-    #
-    # Populate _TavernaIOData_ objects for specified type: value +source+'+ is for inputs
-    # and +sink+ for outputs
-    #
-    def get_IOData(doc, type)
-      io_data = []
-
-      # Get all sources or sinks and create appropriate objects
-      doc.find("//workflow/components/dataflows/dataflow[@role='top']/#{type}s/#{type}").each do |node|
-        name = ''
-        descriptions = []
-        examples = []
-
-        node.each_element do |n|
-          if n.name.eql? "name"
-            name = n.children[0].to_s
-          elsif n.name.eql? "descriptions"
-            n.each_element do |d|
-              descriptions << d.children[0].to_s
-            end if n.children?
-          elsif n.name.eql? "examples"
-            n.each_element do |e|
-              examples << e.children[0].to_s
-            end if n.children?
-          end
-        end
-
-        io_data << TavernaIOData.new(name, descriptions, examples)
-      end
-
-      io_data
-    end
-
-
-    #
-    # Populate _TavernaUser_ object for specified user resource
-    #
-    def get_user(user_uri)
-      doc = XML::Document.file(user_uri)
-      user = TavernaUser.new(doc.find_first("/user/name").content,
-                             doc.find_first("/user/description").content,
-                             doc.find_first("/user/email").content,
-                             doc.find_first("/user/avatar").attributes['uri'],
-                             doc.find_first("/user/website").content,
-                             doc.find_first("/user/created-at").content)
-      user
-    end
-
-
-
-  end
-
-
-
-  #
-  # Contains all available information about a workflow: _input_type_, _xml_uri_,
-  # _title_, _description_,_inputs_, _outputs_ and _user_. The _xml_uri_ specifies
-  # the XML description on myExperiment and not the XML of the workflow itself.
-  # _input_type_ specifies the kind of input. Currently, either "myexperiment"
-  # (myExperiment's xml uri) or "t2flow" (filename)
-  #
-  class TavernaWorkflow
-    
-    # possible input types
-    MY_EXPERIMENT = 'myexperiment'
-    T2_FLOW = 't2flow'
-
-    attr_reader(:input_type, :xml_uri, :title, :description, :inputs, :outputs, :user)
-
-    def initialize(input_type, xml_uri, title, description, inputs, outputs, user)
-      @input_type = input_type
-      @xml_uri = xml_uri
-      @title = title
-      @description = description
-      @inputs = inputs
-      @outputs = outputs
-      @user = user
-    end
-
-  end
-
-
-  #
-  # Contains all available information about an input or output: name, descriptions
-  # and examples. The last two are lists.
-  #--
-  # Currently both inputs and outputs contain the same information. If that
-  # changes we can subclass this one.
-  #
-  class TavernaIOData
-    attr_reader(:name, :descriptions, :examples)
-
-    def initialize(name, descriptions, examples)
-      @name = name
-      @descriptions = descriptions
-      @examples = examples
-    end
-
-  end
-
-
-  #
-  # Contains all available information about an input or output: name, descriptions
-  # and examples. The last two are lists.
-  #
-  class TavernaUser
-    attr_reader(:name, :description, :email, :avatar, :website, :created_at)
-
-    def initialize(name, description, email, avatar, website, created_at)
-      @name = name
-      @description = description
-      @email = email
-      @avatar = avatar
-      @website = website
-      @created_at = created_at
-    end
-
-  end
-
-
-
-end
-