t2-server 0.5.2 → 0.5.3

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Files changed (8) hide show
  1. data/CHANGES.rdoc +4 -0
  2. data/README.rdoc +1 -1
  3. data/lib/t2-server.rb +1 -1
  4. data/lib/t2-server/run.rb +16 -12
  5. data/test/tc_run.rb +3 -2
  6. data/test/workflows/empty_list.t2flow +22 -11
  7. data/test/workflows/empty_list_input.baclava +86 -77
  8. metadata +4 -4
data/CHANGES.rdoc CHANGED
@@ -1,5 +1,9 @@
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  = Changes log for the T2 Ruby Gem
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+ == Version 0.5.3
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+
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+ * Fix an issue with singleton value/empty list confusion for output ports.
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+
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  == Version 0.5.2
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  * Fix two issues with the retrieving of workflow outputs.
data/README.rdoc CHANGED
@@ -1,7 +1,7 @@
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  = Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem
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  Authors:: Robert Haines
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- Gem Version:: 0.5.2
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+ Gem Version:: 0.5.3
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  API Version:: 2.2a1
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  Contact:: mailto:rhaines@manchester.ac.uk
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  URL:: http://taverna.sourceforge.net/
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 = "0.5.2"
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+ GEM_VERSION = "0.5.3"
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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
data/lib/t2-server/run.rb CHANGED
@@ -452,22 +452,26 @@ module T2Server
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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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-
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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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+ # if at the top level we need to check if the port represents a list
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+ # or a singleton value
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+ if top
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+ lists, items = ls("out")
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+ if items.include? output
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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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  end
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+ # we're not at the top level so 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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+ # build up lists of results
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+ result = []
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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, false)}
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data/test/tc_run.rb CHANGED
@@ -90,8 +90,9 @@ class TestRun < Test::Unit::TestCase
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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("OUT"), [[["boo"]], [["", "hello"]],
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- [], [[], ["test"], []]])
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+ assert_equal(@run.get_output("SINGLE"), [])
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+ assert_equal(@run.get_output("MANY"), [[], [["Hello", ""]], [[], ["test"],
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+ []], [["boo"]]])
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  # run with baclava output
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  @run = T2Server::Run.create($address, $wkf_hello)
data/test/workflows/empty_list.t2flow CHANGED
@@ -1,12 +1,23 @@
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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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+ <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="373bb615-7dd3-46b4-9e3c-ee38e7460403" role="top"><name>Workflow1</name><inputPorts><port><name>MANY_IN</name><depth>3</depth><granularDepth>3</granularDepth><annotations /></port><port><name>SINGLE_IN</name><depth>1</depth><granularDepth>1</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>MANY</name><annotations /></port><port><name>SINGLE</name><annotations /></port></outputPorts><processors /><conditions /><datalinks><datalink><sink type="dataflow"><port>MANY</port></sink><source type="dataflow"><port>MANY_IN</port></source></datalink><datalink><sink type="dataflow"><port>SINGLE</port></sink><source type="dataflow"><port>SINGLE_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><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>373bb615-7dd3-46b4-9e3c-ee38e7460403</identification>
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+ </annotationBean>
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+ <date>2010-11-09 13:50:13.127 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>
data/test/workflows/empty_list_input.baclava CHANGED
@@ -1,77 +1,86 @@
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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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-
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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="MANY_IN">
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+ <b:myGridDataDocument lsid="" syntactictype="l(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: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="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 />
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+ </b:dataElement>
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+ <b:dataElement lsid="" index="1">
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+ <b:dataElementData>SGVsbG8=</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>
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+ <b:partialOrder lsid="" type="list" index="3">
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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:itemList>
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+ </b:partialOrder>
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+ </b:myGridDataDocument>
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+ </b:dataThing>
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+ <b:dataThing key="SINGLE_IN">
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+ <b:myGridDataDocument lsid="" syntactictype="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: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: 15
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+ hash: 13
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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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- - 2
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- version: 0.5.2
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+ - 3
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+ version: 0.5.3
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  platform: ruby
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  authors:
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  - Robert Haines
@@ -15,7 +15,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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18
- date: 2010-11-05 00:00:00 +00:00
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+ date: 2010-11-09 00:00:00 +00:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency