t2-server 0.5.1 → 0.5.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/CHANGES.rdoc +5 -0
- data/README.rdoc +1 -1
- data/lib/t2-server.rb +1 -1
- data/lib/t2-server/run.rb +42 -35
- data/test/tc_run.rb +10 -11
- data/test/ts_t2server.rb +2 -2
- data/test/workflows/empty_list.t2flow +12 -0
- data/test/workflows/empty_list_input.baclava +77 -0
- metadata +6 -6
- data/test/workflows/demonstration_of_configurable_iteration_114130.t2flow +0 -335
- data/test/workflows/list_input.baclava +0 -16
data/CHANGES.rdoc
CHANGED
data/README.rdoc
CHANGED
data/lib/t2-server.rb
CHANGED
@@ -43,7 +43,7 @@ require 't2-server/run'
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# Taverna 2 Server instance.
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module T2Server
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# The version of this library
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-
GEM_VERSION = "0.5.
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+
GEM_VERSION = "0.5.2"
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# The version of the Taverna 2 Server API that this library can interface with
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API_VERSION = "2.2a1"
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end
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data/lib/t2-server/run.rb
CHANGED
@@ -137,53 +137,27 @@ module T2Server
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end
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# :call-seq:
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-
# run.get_output(output, refs=false) -> list
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# run.get_output(output, refs=false) -> string or list
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#
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# Return the values of the workflow output port _output_. These are
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-
# returned as a list of strings
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#
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# returned as a list of strings or, if the output port represents a
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# singleton value, then a string returned. By default this method returns
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# the actual data from the output port but if _refs_ is set to true then
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# it will instead return URIs to the actual data in the same list format.
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# See also Run#get_output_refs.
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def get_output(output, refs=false)
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output
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result = []
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-
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# look at the contents of the output port
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-
lists, items = ls("out/#{output}")
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-
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# if lists and items are empty then it's a single value
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if lists == [] and items == []
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if refs
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result << "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}"
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else
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result << @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}")
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end
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end
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-
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# for each list recurse into it and add the items to the result
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lists.each {|list| result << get_output("#{output}/#{list}", refs)}
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-
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# for each item, add it to the output list
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items.each do |item|
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if refs
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result << "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}/#{item}"
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else
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result << @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}/#{item}")
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end
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end
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result
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_get_output(output, refs)
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end
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# :call-seq:
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-
# run.get_output_refs(output) -> list
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# run.get_output_refs(output) -> string or list
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#
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# Return references (URIs) to the values of the workflow output port
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# _output_. These are returned as a list of URIs
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# represents a singleton
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# _output_. These are returned as a list of URIs or, if the output port
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# represents a singleton value, then a single URI is returned. The URIs
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# are returned as strings.
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def get_output_refs(output)
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-
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_get_output(output, true)
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end
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# :call-seq:
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@@ -476,6 +450,39 @@ module T2Server
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end
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private
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def _get_output(output, refs=false, top=true)
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output.strip_path!
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result = []
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# look at the contents of the output port
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lists, items = ls("out/#{output}")
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# if lists and items are empty then it's an empty list
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# although it could be a single value if we're at the top level
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if top and lists == [] and items == []
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# as we are at the top level, just return the single value
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if refs
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return "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}"
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else
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return @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}")
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end
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end
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# for each list recurse into it and add the items to the result
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lists.each {|list| result << _get_output("#{output}/#{list}", refs, false)}
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# for each item, add it to the output list
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items.each do |item|
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if refs
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result << "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}/#{item}"
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else
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result << @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}/#{item}")
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end
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end
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result
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end
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def get_attributes(desc)
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# first parse out the basic stuff
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links = parse_description(desc)
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data/test/tc_run.rb
CHANGED
@@ -58,7 +58,7 @@ class TestRun < Test::Unit::TestCase
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# exitcode and output
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assert_instance_of(Fixnum, @run.exitcode)
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assert_equal(@run.get_output("Message"),
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assert_equal(@run.get_output("Message"), "Hello, World!")
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assert_raise(T2Server::AccessForbiddenError) do
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@run.get_output("wrong!")
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end
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@@ -79,24 +79,23 @@ class TestRun < Test::Unit::TestCase
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@run.wait
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end
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# run that returns list of lists
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# run that returns list of lists, some empty, using baclava for input
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@run = T2Server::Run.create($address, $wkf_lists)
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assert_nothing_raised(T2Server::AttributeNotFoundError) do
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@run.upload_baclava_file($list_input)
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end
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@run.start
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assert(@run.running?)
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assert_nothing_raised(T2Server::RunStateError) do
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@run.wait
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end
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assert_equal(@run.get_output("
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-
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["square green rabbit ", "square red cat "]])
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assert_equal(@run.get_output("OUT"), [[["boo"]], [["", "hello"]],
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[], [[], ["test"], []]])
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# run with baclava
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@run = T2Server::Run.create($address, $
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# run with baclava output
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@run = T2Server::Run.create($address, $wkf_hello)
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assert_nothing_raised(T2Server::AttributeNotFoundError) do
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@run.upload_baclava_file($baclava_in)
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end
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assert_nothing_raised(T2Server::AttributeNotFoundError) do
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@run.set_baclava_output
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end
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data/test/ts_t2server.rb
CHANGED
@@ -51,8 +51,8 @@ require 'tc_paths'
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if $address != ""
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$wkf_hello = File.read("test/workflows/hello.t2flow")
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$wkf_input = File.read("test/workflows/pipelined_list_iteration_902021.t2flow")
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$wkf_lists = File.read("test/workflows/
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$
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$wkf_lists = File.read("test/workflows/empty_list.t2flow")
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$list_input = "test/workflows/empty_list_input.baclava"
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require 'tc_server'
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require 'tc_run'
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@@ -0,0 +1,12 @@
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1
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="536f469a-fd80-4efa-8d76-6cb2514123ec" role="top"><name>Workflow1</name><inputPorts><port><name>IN</name><depth>2</depth><granularDepth>2</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>OUT</name><annotations /></port></outputPorts><processors /><conditions /><datalinks><datalink><sink type="dataflow"><port>OUT</port></sink><source type="dataflow"><port>IN</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationAssertions>
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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<identification>536f469a-fd80-4efa-8d76-6cb2514123ec</identification>
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</annotationBean>
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<date>2010-11-04 18:00:12.867 GMT</date>
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<creators />
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<curationEventList />
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</annotationAssertions>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
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@@ -0,0 +1,77 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
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<b:dataThing key="IN">
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<b:myGridDataDocument lsid="" syntactictype="l(l('null'))">
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<s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
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<b:partialOrder lsid="" type="list">
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<b:relationList>
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<b:relation parent="0" child="1" />
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<b:relation parent="1" child="2" />
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<b:relation parent="2" child="3" />
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</b:relationList>
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<b:itemList>
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<b:partialOrder lsid="" type="list" index="0">
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<b:relationList>
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<b:relation parent="0" child="1" />
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<b:relation parent="1" child="2" />
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</b:relationList>
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<b:itemList>
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<b:partialOrder lsid="" type="list" index="0">
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<b:relationList />
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<b:itemList />
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</b:partialOrder>
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<b:partialOrder lsid="" type="list" index="1">
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<b:relationList />
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<b:itemList>
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<b:dataElement lsid="" index="0">
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<b:dataElementData>dGVzdA==</b:dataElementData>
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</b:dataElement>
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</b:itemList>
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</b:partialOrder>
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<b:partialOrder lsid="" type="list" index="2">
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<b:relationList />
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<b:itemList />
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</b:partialOrder>
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</b:itemList>
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</b:partialOrder>
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<b:partialOrder lsid="" type="list" index="1">
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<b:relationList />
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<b:itemList>
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<b:partialOrder lsid="" type="list" index="0">
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<b:relationList>
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<b:relation parent="0" child="1" />
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</b:relationList>
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<b:itemList>
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<b:dataElement lsid="" index="0">
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<b:dataElementData>aGVsbG8=</b:dataElementData>
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</b:dataElement>
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<b:dataElement lsid="" index="1">
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<b:dataElementData />
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</b:dataElement>
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</b:itemList>
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</b:partialOrder>
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</b:itemList>
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</b:partialOrder>
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<b:partialOrder lsid="" type="list" index="2">
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<b:relationList />
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<b:itemList>
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<b:partialOrder lsid="" type="list" index="0">
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<b:relationList />
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<b:itemList>
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<b:dataElement lsid="" index="0">
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<b:dataElementData>Ym9v</b:dataElementData>
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</b:dataElement>
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</b:itemList>
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</b:partialOrder>
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</b:itemList>
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</b:partialOrder>
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<b:partialOrder lsid="" type="list" index="3">
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<b:relationList />
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<b:itemList />
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</b:partialOrder>
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</b:itemList>
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</b:partialOrder>
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</b:myGridDataDocument>
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</b:dataThing>
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</b:dataThingMap>
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metadata
CHANGED
@@ -1,13 +1,13 @@
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--- !ruby/object:Gem::Specification
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name: t2-server
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version: !ruby/object:Gem::Version
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hash:
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hash: 15
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prerelease: false
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segments:
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- 0
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- 5
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-
-
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version: 0.5.
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- 2
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version: 0.5.2
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platform: ruby
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authors:
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- Robert Haines
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@@ -15,7 +15,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2010-
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date: 2010-11-05 00:00:00 +00:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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@@ -75,9 +75,9 @@ files:
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- test/tc_server.rb
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- test/tc_paths.rb
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- test/tc_run.rb
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-
- test/workflows/list_input.baclava
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- test/workflows/pipelined_list_iteration_902021.t2flow
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-
- test/workflows/
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+
- test/workflows/empty_list_input.baclava
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- test/workflows/empty_list.t2flow
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- test/workflows/hello.t2flow
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- test/ts_t2server.rb
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- README.rdoc
|
@@ -1,335 +0,0 @@
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1
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-
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="be152f54-e4a7-4324-9ce6-44438c5daed7" role="top"><name>Demonstrationofconfigurableiteration</name><inputPorts /><outputPorts><port><name>Output</name><annotations /></port></outputPorts><processors><processor><name>Colours</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
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-
<value>red ,green ,</value>
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-
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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<maxJobs>1</maxJobs>
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-
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
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6
|
-
<backoffFactor>1.0</backoffFactor>
|
7
|
-
<initialDelay>0</initialDelay>
|
8
|
-
<maxDelay>0</maxDelay>
|
9
|
-
<maxRetries>0</maxRetries>
|
10
|
-
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>Animals</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
|
11
|
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<value>cat ,rabbit ,</value>
|
12
|
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</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
|
13
|
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<maxJobs>1</maxJobs>
|
14
|
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
|
15
|
-
<backoffFactor>1.0</backoffFactor>
|
16
|
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<initialDelay>0</initialDelay>
|
17
|
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<maxDelay>0</maxDelay>
|
18
|
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<maxRetries>0</maxRetries>
|
19
|
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>Shapes</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
|
20
|
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<value>square ,circular ,triangular ,</value>
|
21
|
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</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
|
22
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<maxJobs>1</maxJobs>
|
23
|
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
|
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<backoffFactor>1.0</backoffFactor>
|
25
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<initialDelay>0</initialDelay>
|
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<maxDelay>0</maxDelay>
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<maxRetries>0</maxRetries>
|
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>ColoursLisr</name><inputPorts><port><name>string</name><depth>0</depth></port></inputPorts><outputPorts><port><name>split</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="string" to="string" /></inputMap><outputMap><map from="split" to="split" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
29
|
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<localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
|
30
|
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<script>List split = new ArrayList();
|
31
|
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if (!string.equals("")) {
|
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String regexString = ",";
|
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if (regex != void) {
|
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|
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regexString = regex;
|
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|
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}
|
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|
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String[] result = string.split(regexString);
|
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|
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for (int i = 0; i < result.length; i++) {
|
38
|
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split.add(result[i]);
|
39
|
-
}
|
40
|
-
}
|
41
|
-
</script>
|
42
|
-
<dependencies />
|
43
|
-
<classLoaderSharing>workflow</classLoaderSharing>
|
44
|
-
<localDependencies />
|
45
|
-
<artifactDependencies />
|
46
|
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<inputs>
|
47
|
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
48
|
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<handledReferenceSchemes />
|
49
|
-
<translatedElementType>java.lang.String</translatedElementType>
|
50
|
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<allowsLiteralValues>true</allowsLiteralValues>
|
51
|
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<name>string</name>
|
52
|
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<depth>0</depth>
|
53
|
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<mimeTypes>
|
54
|
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<string>'text/plain'</string>
|
55
|
-
</mimeTypes>
|
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|
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
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|
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
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|
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<handledReferenceSchemes />
|
59
|
-
<translatedElementType>java.lang.String</translatedElementType>
|
60
|
-
<allowsLiteralValues>true</allowsLiteralValues>
|
61
|
-
<name>regex</name>
|
62
|
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<depth>0</depth>
|
63
|
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<mimeTypes>
|
64
|
-
<string>'text/plain'</string>
|
65
|
-
</mimeTypes>
|
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|
-
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
67
|
-
</inputs>
|
68
|
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<outputs>
|
69
|
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
70
|
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<granularDepth>1</granularDepth>
|
71
|
-
<name>split</name>
|
72
|
-
<depth>1</depth>
|
73
|
-
<mimeTypes>
|
74
|
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<string>l('text/plain')</string>
|
75
|
-
</mimeTypes>
|
76
|
-
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
77
|
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</outputs>
|
78
|
-
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
|
79
|
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<maxJobs>1</maxJobs>
|
80
|
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
|
81
|
-
<backoffFactor>1.0</backoffFactor>
|
82
|
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<initialDelay>1000</initialDelay>
|
83
|
-
<maxDelay>5000</maxDelay>
|
84
|
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<maxRetries>0</maxRetries>
|
85
|
-
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>AnimalsList</name><inputPorts><port><name>string</name><depth>0</depth></port></inputPorts><outputPorts><port><name>split</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="string" to="string" /></inputMap><outputMap><map from="split" to="split" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
86
|
-
<localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
|
87
|
-
<script>List split = new ArrayList();
|
88
|
-
if (!string.equals("")) {
|
89
|
-
String regexString = ",";
|
90
|
-
if (regex != void) {
|
91
|
-
regexString = regex;
|
92
|
-
}
|
93
|
-
String[] result = string.split(regexString);
|
94
|
-
for (int i = 0; i < result.length; i++) {
|
95
|
-
split.add(result[i]);
|
96
|
-
}
|
97
|
-
}
|
98
|
-
</script>
|
99
|
-
<dependencies />
|
100
|
-
<classLoaderSharing>workflow</classLoaderSharing>
|
101
|
-
<localDependencies />
|
102
|
-
<artifactDependencies />
|
103
|
-
<inputs>
|
104
|
-
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
105
|
-
<handledReferenceSchemes />
|
106
|
-
<translatedElementType>java.lang.String</translatedElementType>
|
107
|
-
<allowsLiteralValues>true</allowsLiteralValues>
|
108
|
-
<name>string</name>
|
109
|
-
<depth>0</depth>
|
110
|
-
<mimeTypes>
|
111
|
-
<string>'text/plain'</string>
|
112
|
-
</mimeTypes>
|
113
|
-
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
114
|
-
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
115
|
-
<handledReferenceSchemes />
|
116
|
-
<translatedElementType>java.lang.String</translatedElementType>
|
117
|
-
<allowsLiteralValues>true</allowsLiteralValues>
|
118
|
-
<name>regex</name>
|
119
|
-
<depth>0</depth>
|
120
|
-
<mimeTypes>
|
121
|
-
<string>'text/plain'</string>
|
122
|
-
</mimeTypes>
|
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|
-
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
124
|
-
</inputs>
|
125
|
-
<outputs>
|
126
|
-
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
127
|
-
<granularDepth>1</granularDepth>
|
128
|
-
<name>split</name>
|
129
|
-
<depth>1</depth>
|
130
|
-
<mimeTypes>
|
131
|
-
<string>l('text/plain')</string>
|
132
|
-
</mimeTypes>
|
133
|
-
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
134
|
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</outputs>
|
135
|
-
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
|
136
|
-
<maxJobs>1</maxJobs>
|
137
|
-
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
|
138
|
-
<backoffFactor>1.0</backoffFactor>
|
139
|
-
<initialDelay>1000</initialDelay>
|
140
|
-
<maxDelay>5000</maxDelay>
|
141
|
-
<maxRetries>0</maxRetries>
|
142
|
-
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ShapesList</name><inputPorts><port><name>string</name><depth>0</depth></port></inputPorts><outputPorts><port><name>split</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="string" to="string" /></inputMap><outputMap><map from="split" to="split" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
143
|
-
<localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
|
144
|
-
<script>List split = new ArrayList();
|
145
|
-
if (!string.equals("")) {
|
146
|
-
String regexString = ",";
|
147
|
-
if (regex != void) {
|
148
|
-
regexString = regex;
|
149
|
-
}
|
150
|
-
String[] result = string.split(regexString);
|
151
|
-
for (int i = 0; i < result.length; i++) {
|
152
|
-
split.add(result[i]);
|
153
|
-
}
|
154
|
-
}
|
155
|
-
</script>
|
156
|
-
<dependencies />
|
157
|
-
<classLoaderSharing>workflow</classLoaderSharing>
|
158
|
-
<localDependencies />
|
159
|
-
<artifactDependencies />
|
160
|
-
<inputs>
|
161
|
-
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
162
|
-
<handledReferenceSchemes />
|
163
|
-
<translatedElementType>java.lang.String</translatedElementType>
|
164
|
-
<allowsLiteralValues>true</allowsLiteralValues>
|
165
|
-
<name>string</name>
|
166
|
-
<depth>0</depth>
|
167
|
-
<mimeTypes>
|
168
|
-
<string>'text/plain'</string>
|
169
|
-
</mimeTypes>
|
170
|
-
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
171
|
-
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
172
|
-
<handledReferenceSchemes />
|
173
|
-
<translatedElementType>java.lang.String</translatedElementType>
|
174
|
-
<allowsLiteralValues>true</allowsLiteralValues>
|
175
|
-
<name>regex</name>
|
176
|
-
<depth>0</depth>
|
177
|
-
<mimeTypes>
|
178
|
-
<string>'text/plain'</string>
|
179
|
-
</mimeTypes>
|
180
|
-
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
181
|
-
</inputs>
|
182
|
-
<outputs>
|
183
|
-
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
184
|
-
<granularDepth>1</granularDepth>
|
185
|
-
<name>split</name>
|
186
|
-
<depth>1</depth>
|
187
|
-
<mimeTypes>
|
188
|
-
<string>l('text/plain')</string>
|
189
|
-
</mimeTypes>
|
190
|
-
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
191
|
-
</outputs>
|
192
|
-
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
|
193
|
-
<maxJobs>1</maxJobs>
|
194
|
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