mannie-taverna-t2flow 0.0.5 → 0.1.0
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- data/README.rdoc +1 -1
- data/Release_Notes.rdoc +6 -5
- data/lib/t2flow/model.rb +110 -40
- data/lib/t2flow/parser.rb +12 -0
- metadata +2 -2
data/README.rdoc
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= Taverna[http://taverna.sourceforge.net] 2 Interaction Gem
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Authors:: Emmanuel Tagarira, David Withers
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Version:: 0.0
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Version:: 0.1.0
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Contact:: mailto:emmanuel.tagarira@student.manchester.ac.uk
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URL:: http://taverna.sourceforge.net/
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Licence:: LGPL 3 (See LICENCE or http://www.gnu.org/licenses/lgpl.html)
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data/Release_Notes.rdoc
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= Version 0.0
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== Bug fixes
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- BioMart services now return a type value instead of nil when processor.type is invoked.
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= Version 0.1.0
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Released:: Monday, September 14, 2009
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== Added Functionality
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- Retrieval of processors directly connected/linked to the given processor.
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=== New instance method in T2Flow::Model
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get_processor_links(processor)
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=== New supporting object T2Flow::ProcessorLinks
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data/lib/t2flow/model.rb
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# Retrieve ALL the processors containing beanshells within the workflow.
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def beanshells
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}
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return beanshells
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self.all_processors.select { |x| x.type == "beanshell" }
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end
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# Retrieve ALL processors of that are webservices WITHIN the model.
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def web_services
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self.all_processors.select { |x| x.type =~ /wsdl|soaplab|biomoby/i }
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end
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# Retrieve the datalinks from the top level of a nested workflow.
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# Retrieve ALL the datalinks within a nested workflow
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def all_datalinks
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links = []
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@dataflows.each { |dataflow|
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links << link
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}
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}
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return links
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@dataflows.each { |dataflow| links << dataflow.datalinks }
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return links.flatten
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end
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# Retrieve the annotations specific to the workflow. This does not return
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# Retrieve ALL the processors found in a nested workflow
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def all_processors
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procs =[]
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@dataflows.each { |dataflow|
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procs << proc
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}
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}
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return procs
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@dataflows.each { |dataflow| procs << dataflow.processors }
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return procs.flatten
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end
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# Retrieve the sources(inputs) to the workflow
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# Retrieve ALL the sources(inputs) within the workflow
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def all_sources
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sources =[]
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@dataflows.each { |dataflow|
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sources << source
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}
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}
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return sources
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@dataflows.each { |dataflow| sources << dataflow.sources }
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return sources.flatten
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end
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# Retrieve the sinks(outputs) to the workflow
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# Retrieve ALL the sinks(outputs) within the workflow
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def all_sinks
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sinks =[]
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@dataflows.each { |dataflow|
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sinks << sink
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}
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}
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return sinks
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@dataflows.each { |dataflow| sinks << dataflow.sinks }
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return sinks.flatten
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end
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# Retrieve the unique dataflow ID for the top level dataflow.
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def model_id
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self.main.dataflow_id
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end
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# For the given dataflow, return the beanshells and/or services which
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# have direct links to or from the given processor.
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# If no dataflow is specified, the top-level dataflow is used.
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# This does a recursive search in nested workflows.
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# == Usage
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# my_processor = model.processor[0]
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# linked_processors = model.get_processors_linked_to(my_processor)
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# processors_feeding_into_my_processor = linked_processors.sources
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# processors_feeding_from_my_processor = linked_processors.sinks
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def get_processor_links(processor)
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return nil unless processor
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proc_links = ProcessorLinks.new
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# SOURCES
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sources = self.all_datalinks.select { |x| x.sink =~ /#{processor.name}:.+/ }
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proc_links.sources = []
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# SINKS
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sinks = self.all_datalinks.select { |x| x.source =~ /#{processor.name}:.+/ }
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proc_links.sinks = []
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temp_sinks = []
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sinks.each { |x| temp_sinks << x.sink }
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# Match links by port into format
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# my_port:name_of_link_im_linked_to:its_port
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sources.each do |connection|
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link = connection.sink
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connected_proc_name = link.split(":")[0]
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my_connection_port = link.split(":")[1]
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if my_connection_port
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source = my_connection_port << ":" << connection.source
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proc_links.sources << source if source.split(":").size == 3
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end
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end
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sinks.each do |connection|
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link = connection.source
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connected_proc_name = link.split(":")[0]
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my_connection_port = link.split(":")[1]
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if my_connection_port
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sink = my_connection_port << ":" << connection.sink
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proc_links.sinks << sink if sink.split(":").size == 3
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end
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end
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return proc_links
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end
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end
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# elements of the workflows; processors, sinks, sources, etc...
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class Dataflow
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# This returns a DataflowAnnotation object.
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attr_accessor :annotations
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# Retrieve the list of processors specific to the dataflow.
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attr_accessor :processors
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# Retrieve the list of datalinks specific to the dataflow.
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attr_accessor :datalinks
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# Retrieve the list of sources specific to the dataflow.
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attr_accessor :sources
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# Retrieve the list of sinks specific to the dataflow.
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attr_accessor :sinks
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# Retrieve the list of coordinations specific to the dataflow.
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attr_accessor :coordinations
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# The unique identifier of the dataflow.
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attr_accessor :dataflow_id
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@processors.select { |x| x.type == "beanshell" }
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end
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end
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# This is the (shim) object within the workflow. This can be a beanshell,
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# a webservice, a workflow, etc...
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# A string for the type of processor, e.g. beanshell, workflow, webservice, etc...
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attr_accessor :type
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# For processors that have type
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# For processors that have type "dataflow", this is the the reference
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# to the dataflow. For all other processor types, this is nil.
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attr_accessor :dataflow_id
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# This is a list of outputs that the processor can produce.
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attr_accessor :outputs
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# For processors of type "arbitrarywsdl", this is the URI to the location
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# of the wsdl file.
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attr_accessor :wsdl
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# For processors of type "arbitrarywsdl", this is the operation invoked.
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attr_accessor :wsdl_operation
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# For soaplab and biomoby services, this is the endpoint URI.
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attr_accessor :endpoint
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# Authority name for the biomoby service.
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attr_accessor :biomoby_authority_name
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# Service name for the biomoby service. This is not necessarily the same
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# as the processors name.
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attr_accessor :biomoby_service_name
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# Category for the biomoby service.
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attr_accessor :biomoby_category
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end
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# This object is returned after invoking model.get_processor_links(processor)
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# . The object contains two lists of processors. Each element consists of:
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# the input or output port the processor uses as a link, the name of the
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# processor being linked, and the port of the processor used for the linking,
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# all seperated by a colon (:) i.e.
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# my_port:name_of_processor:processor_port
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class ProcessorLinks
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# The processors whose output is fed as input into the processor used in
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# model.get_processors_linked_to(processor).
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attr_accessor :sources
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# A list of processors that are fed the output from the processor (used in
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# model.get_processors_linked_to(processor) ) as input.
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attr_accessor :sinks
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end
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# This is the annotation object specific to the dataflow it belongs to.
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# A DataflowAnnotation contains metadata about a given dataflow element.
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data/lib/t2flow/parser.rb
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activity_node.each do |value_node|
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case value_node.name
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when "wsdl"
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processor.wsdl = value_node.content
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when "operation"
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processor.wsdl_operation = value_node.content
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when /endpoint/i
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processor.endpoint = value_node.content
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when /servicename/i
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processor.biomoby_service_name = value_node.content
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when /authorityname/i
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processor.biomoby_authority_name = value_node.content
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when "category"
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processor.biomoby_category = value_node.content
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when "script"
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processor.script = value_node.content
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when "inputs" # ALL ports present in beanshell
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metadata
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--- !ruby/object:Gem::Specification
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name: mannie-taverna-t2flow
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version: !ruby/object:Gem::Version
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version: 0.0
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version: 0.1.0
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platform: ruby
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authors:
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- Emmanuel Tagarira
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@@ -9,7 +9,7 @@ authors:
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autorequire: t2flow
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bindir: bin
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cert_chain:
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date: 2009-09-
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date: 2009-09-14 00:00:00 -07:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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