myexperiment-rest 0.2.6

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  1. data/CHANGES +9 -0
  2. data/LICENSE +23 -0
  3. data/README +33 -0
  4. data/Rakefile +45 -0
  5. data/bin/get_workflow_data.rb +31 -0
  6. data/doc/classes/MyExperimentREST.html +113 -0
  7. data/doc/classes/MyExperimentREST/IOData.html +169 -0
  8. data/doc/classes/MyExperimentREST/IOData.src/M000003.html +20 -0
  9. data/doc/classes/MyExperimentREST/ReadWorkflow.html +184 -0
  10. data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000002.html +39 -0
  11. data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000005.html +41 -0
  12. data/doc/classes/MyExperimentREST/TavernaIOData.html +167 -0
  13. data/doc/classes/MyExperimentREST/TavernaIOData.src/M000006.html +20 -0
  14. data/doc/classes/MyExperimentREST/TavernaIOData.src/M000007.html +20 -0
  15. data/doc/classes/MyExperimentREST/TavernaWorkflow.html +209 -0
  16. data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000005.html +23 -0
  17. data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000006.html +22 -0
  18. data/doc/classes/MyExperimentREST/Workflow.html +172 -0
  19. data/doc/classes/MyExperimentREST/Workflow.src/M000001.html +21 -0
  20. data/doc/classes/MyExperimentREST/Workflows.html +167 -0
  21. data/doc/classes/MyExperimentREST/Workflows.src/M000004.html +41 -0
  22. data/doc/classes/TestReadWorkflow.html +167 -0
  23. data/doc/classes/TestReadWorkflow.src/M000001.html +18 -0
  24. data/doc/classes/TestReadWorkflow.src/M000002.html +24 -0
  25. data/doc/classes/TestReadWorkflow.src/M000003.html +20 -0
  26. data/doc/classes/TestReadWorkflow.src/M000004.html +20 -0
  27. data/doc/created.rid +1 -0
  28. data/doc/files/bin/get_workflow_data_rb.html +116 -0
  29. data/doc/files/lib/myexperiment-rest/my_experiment_rest_rb.html +110 -0
  30. data/doc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
  31. data/doc/files/lib/myexperiment-rest_rb.html +108 -0
  32. data/doc/files/test/test_read_workflow_rb.html +122 -0
  33. data/doc/fr_class_index.html +31 -0
  34. data/doc/fr_file_index.html +29 -0
  35. data/doc/fr_method_index.html +32 -0
  36. data/doc/index.html +24 -0
  37. data/doc/rdoc-style.css +208 -0
  38. data/doc/rdoc/classes/MyExperimentREST.html +117 -0
  39. data/doc/rdoc/classes/MyExperimentREST/TavernaIOData.html +178 -0
  40. data/doc/rdoc/classes/MyExperimentREST/TavernaWorkflow.html +223 -0
  41. data/doc/rdoc/classes/MyExperimentREST/Workflows.html +199 -0
  42. data/doc/rdoc/created.rid +1 -0
  43. data/doc/rdoc/files/CHANGES.html +121 -0
  44. data/doc/rdoc/files/LICENSE.html +133 -0
  45. data/doc/rdoc/files/README.html +148 -0
  46. data/doc/rdoc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
  47. data/doc/rdoc/files/lib/myexperiment-rest_rb.html +108 -0
  48. data/doc/rdoc/fr_class_index.html +30 -0
  49. data/doc/rdoc/fr_file_index.html +31 -0
  50. data/doc/rdoc/fr_method_index.html +29 -0
  51. data/doc/rdoc/index.html +24 -0
  52. data/doc/rdoc/rdoc-style.css +208 -0
  53. data/lib/myexperiment-rest.rb +5 -0
  54. data/lib/myexperiment-rest/myexperiment_rest.rb +146 -0
  55. metadata +133 -0
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data/lib/myexperiment-rest.rb ADDED
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+ require 'myexperiment-rest/myexperiment_rest.rb'
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+
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+ module MyExperimentREST
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+
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+ end
data/lib/myexperiment-rest/myexperiment_rest.rb ADDED
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+ require 'rubygems'
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+ require 'rest_client'
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+ require 'libxml'
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+
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+ module MyExperimentREST
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+
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+ #
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+ # Connects to myExperiment REST API and creates a _TavernaWorkflow_ object.
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+ #
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+ class Workflows
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+ include LibXML
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+
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+ attr_reader(:uri)
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+
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+ #def initialize
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+ #end
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+
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+ # Requires the URI of the workflow in the repository as a String.
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+ def read(uri)
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+
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+ workflow_id = ''
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+ workflow_version = ''
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+
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+ # Get workflow id
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+ uri_id = uri.match(/workflows\/(\d+)/)
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+ if uri_id != nil
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+ workflow_id = uri_id[1]
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+ else
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+ raise "Could not match workflow id."
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+ end
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+
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+ # Get workflow version if it exists
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+ uri_version = uri.match(/version=(\d+)/)
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+ if uri_version != nil
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+ workflow_version = uri_version[1]
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+ end
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+
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+ # Get workflow resource information -- if version is empty it returns the current version
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+ response = RestClient.get('http://www.myexperiment.org/workflow.xml', {:params => {'id' => "#{workflow_id}",
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+ 'version' => "#{workflow_version}",
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+ 'elements' => 'title,description,content-uri,components'} } )
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+
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+ populate_workflow(response)
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+ end
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+
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+
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+ private
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+
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+ # Acquire data from XML response and instantiate a _Taverna_Workflow_ object
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+ def populate_workflow(response)
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+ doc = XML::Document.string(response)
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+ wkf_xml_uri = doc.find_first("/workflow/content-uri").content
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+ wkf_title = doc.find_first("/workflow/title").content
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+ wkf_descr = doc.find_first("/workflow/description").content
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+ wkf_inputs = get_IOData(doc, "source")
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+ wkf_outputs = get_IOData(doc, "sink")
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+
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+ TavernaWorkflow.new(TavernaWorkflow::MY_EXPERIMENT, wkf_xml_uri, wkf_title, wkf_descr, wkf_inputs, wkf_outputs)
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+
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+ end
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+
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+
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+ #
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+ # Populate _Taverna_IOData_ objects for specified type: value +source+'+ is for inputs
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+ # and +sink+ for outputs
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+ #
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+ def get_IOData(doc, type)
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+ io_data = []
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+
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+ # Get all sources or sinks and create appropriate objects
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+ doc.find("//workflow/components/dataflows/dataflow[@role='top']/#{type}s/#{type}").each do |node|
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+ name = ''
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+ descriptions = []
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+ examples = []
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+
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+ node.each_element do |n|
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+ if n.name.eql? "name"
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+ name = n.children[0].to_s
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+ elsif n.name.eql? "descriptions"
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+ n.each_element do |d|
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+ descriptions << d.children[0].to_s
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+ end if n.children?
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+ elsif n.name.eql? "examples"
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+ n.each_element do |e|
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+ examples << e.children[0].to_s
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+ end if n.children?
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+ end
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+ end
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+
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+ io_data << TavernaIOData.new(name, descriptions, examples)
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+ end
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+
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+ io_data
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+ end
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+
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+
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+ end
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+
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+
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+ #
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+ # Contains all available information about a workflow: _input_type_, _xml_uri_, _title_, _description_,
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+ # _inputs_ and _outputs_. The _xml_uri_ specifies the XML description on myExperiment and
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+ # not the XML of the workflow itself. _input_type_ specifies the kind of input. Currently,
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+ # either "myexperiment" (myExperiment's xml uri) or "t2flow" (filename)
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+ #
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+ class TavernaWorkflow
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+
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+ # possible input types
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+ MY_EXPERIMENT = 'myexperiment'
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+ T2_FLOW = 't2flow'
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+
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+ attr_reader(:input_type, :xml_uri, :title, :description, :inputs, :outputs)
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+
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+ def initialize(input_type, xml_uri, title, description, inputs, outputs)
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+ @input_type = input_type
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+ @xml_uri = xml_uri
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+ @title = title
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+ @description = description
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+ @inputs = inputs
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+ @outputs = outputs
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+ end
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+
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+ end
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+
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+
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+ #
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+ # Contains all available information about an input or output: name, descriptions
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+ # and examples. The last two are lists.
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+ #--
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+ # Currently both inputs and outputs contain the same information. If that
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+ # changes we can subclass this one.
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+ #
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+ class TavernaIOData
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+ attr_reader(:name, :descriptions, :examples)
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+
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+ def initialize(name, descriptions, examples)
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+ @name = name
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+ @descriptions = descriptions
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+ @examples = examples
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+ end
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+
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+ end
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+
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+
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+ end
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+
metadata ADDED
@@ -0,0 +1,133 @@
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+ --- !ruby/object:Gem::Specification
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+ name: myexperiment-rest
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+ version: !ruby/object:Gem::Version
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+ hash: 27
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+ prerelease:
6
+ segments:
7
+ - 0
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+ - 2
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+ - 6
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+ version: 0.2.6
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+ platform: ruby
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+ authors:
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+ - Konstantinos Karasavvas
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+
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+ date: 2011-07-20 00:00:00 Z
19
+ dependencies:
20
+ - !ruby/object:Gem::Dependency
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+ name: rest-client
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+ prerelease: false
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+ requirement: &id001 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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+ - 0
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+ version: "0"
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+ type: :runtime
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+ version_requirements: *id001
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+ description: This is a simple library to access data on myExperiment via its REST API. Currently supports a subset of the workflow information available.
35
+ email: kostas.karasavvas@nbic.nl
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+ executables:
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+ - get_workflow_data.rb
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+ extensions: []
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+
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+ extra_rdoc_files:
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+ - README
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+ - LICENSE
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+ - CHANGES
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+ files:
45
+ - LICENSE
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+ - README
47
+ - CHANGES
48
+ - Rakefile
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+ - bin/get_workflow_data.rb
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+ - lib/myexperiment-rest.rb
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+ - lib/myexperiment-rest/myexperiment_rest.rb
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+ - doc/rdoc-style.css
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+ - doc/fr_file_index.html
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+ - doc/classes/TestReadWorkflow.html
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+ - doc/classes/MyExperimentREST/IOData.src/M000003.html
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+ - doc/classes/MyExperimentREST/TavernaIOData.html
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+ - doc/classes/MyExperimentREST/Workflows.html
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+ - doc/classes/MyExperimentREST/TavernaWorkflow.html
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+ - doc/classes/MyExperimentREST/ReadWorkflow.html
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+ - doc/classes/MyExperimentREST/Workflows.src/M000004.html
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+ - doc/files/test/test_read_workflow_rb.html
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+ - doc/rdoc/files/LICENSE.html
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+ - doc/rdoc/files/README.html
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+ homepage:
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+ licenses: []
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+ - lib
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+ - - ">="
120
+ - !ruby/object:Gem::Version
121
+ hash: 3
122
+ segments:
123
+ - 0
124
+ version: "0"
125
+ requirements: []
126
+
127
+ rubyforge_project:
128
+ rubygems_version: 1.7.2
129
+ signing_key:
130
+ specification_version: 3
131
+ summary: This is a simple library to access data on myExperiment via its REST API. Currently supports a subset of the workflow information available.
132
+ test_files: []
133
+