t2-server 0.5.3 → 0.6.0

data/CHANGES.rdoc

@@ -1,5 +1,18 @@
 = Changes log for the T2 Ruby Gem
 
+== Version 0.6.0
+
+* Add a new API call Run#get_output_ports
+* Remove Run#ls from the API.
+* Refactor the code that builds output port lists.
+* Update and streamline test suite.
+* Parameterize the Rakefile for use in CI.
+* Return dates as instances of class Time.
+* Allow expiry dates to be specified in human readable formats.
+* Workaround for CXF bug upon server start-up.
+* t2-run-workflow: accept files as inputs.
+* Tabulate run information.
+
 == Version 0.5.3
 
 * Fix an issue with singleton value/empty list confusion for output ports.

data/README.rdoc

@@ -1,7 +1,7 @@
 = Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem
 
 Authors::     Robert Haines
-Gem Version:: 0.5.3
+Gem Version:: 0.6.0
 API Version:: 2.2a1
 Contact::     mailto:rhaines@manchester.ac.uk
 URL::         http://taverna.sourceforge.net/

data/bin/t2-run-workflow

@@ -35,29 +35,9 @@ require 'rubygems'
 require 't2-server'
 require 'optparse'
 
-# go through the outputs and either print the contents
-# out or save them to a file.
-# if the output is a list, it appears as a directory so
-# all the individual entries must be grabbed from there.
-def get_outputs(run, refs)
-  # get a list of the outputs
-  lists, items = run.ls("out")
-
-  # go through the lists
-  lists.each do |l|
-    print "          #{l} -> "
-    p run.get_output("#{l}", refs)
-  end
-
-  # go through the singletons
-  items.each do |i|
-    print "          #{i} -> "
-    p run.get_output("#{i}", refs)
-  end
-end
-
 # set up options
 inputs  = {}
+files = {}
 wkf_file = ""
 output_refs = false
 baclava_out = ""
@@ -76,6 +56,11 @@ opts = OptionParser.new do |opt|
     input, value = val.chomp.split(':', 2)
     inputs[input] = value
   end
+  opt.on("-f INPUT:FILE", "--input-file=INPUT:FILE",
+    "Set input port INPUT to use the contents of FILE as its input") do |val|
+      input, filename = val.chomp.split(':', 2)
+      files[input] = filename
+    end
   opt.on("-b BACLAVA", "--baclava-in=BACLAVA", "Set baclava file for input port values") do |val|
     inputs[:baclava] = val
   end
@@ -143,6 +128,12 @@ else
     puts "Set input '#{input}' to #{value}"
     run.set_input(input, value)
   end
+  
+  files.each do |input, file|
+    name = file.split("/")[-1];
+    puts "Set input '#{input}' to use file '#{name}'"
+    run.upload_input_file(input, file)
+  end
 end
 
 # output baclava?
@@ -170,8 +161,12 @@ if exitcd == 0
     end
     puts "Baclava file written to '#{baclava_out}'"
   else
+    # go through the outputs and print them out
     puts "Outputs:"
-    get_outputs(run, output_refs)
+    run.get_output_ports.each do |o|
+      print "          #{o} -> "
+      p run.get_output("#{o}", output_refs)
+    end
   end
 end
 

data/bin/t2-server-info

@@ -34,6 +34,7 @@
 require 'rubygems'
 require 't2-server'
 require 'optparse'
+require 'hirb'
 
 opts = OptionParser.new do |opt|
   opt.banner = "Usage: t2-server-info [options] server-address"
@@ -70,10 +71,12 @@ begin
   runs = server.runs
   print "No. of runs: #{runs.length}\n"
   if runs.length > 0
-    print "   Run list: #{runs[0].uuid} - #{runs[0].expiry}\n"
-    runs[1..-1].each do |run|
-      print "             #{run.uuid} - #{run.expiry}\n"
-    end
+    puts (Hirb::Helpers::ObjectTable.render runs,
+      :fields=>[:uuid, :status, :expiry],
+      :headers=>{:uuid=>'Run ID', :status=>'Status', :expiry=>'Expiry time (local)'},
+      :filters=>{:expiry=>[:strftime, "%H:%M:%S %d/%m/%Y"]},
+      :max_fields=>{:expiry=>19},
+      :description=>false)
   end
 rescue T2Server::T2ServerError => e
   puts e

data/lib/t2-server/run.rb

@@ -32,6 +32,7 @@
 
 require 'rubygems'
 require 'libxml'
+require 'time'
 
 module T2Server
 
@@ -136,6 +137,15 @@ module T2Server
       @server.set_run_input_file(self, input, filename)
     end
 
+    # :call-seq:
+    #   run.get_output_ports -> list
+    #
+    # Return a list of all the output ports
+    def get_output_ports
+      lists, items = _ls_ports("out")
+      items + lists
+    end
+
     # :call-seq:
     #   run.get_output(output, refs=false) -> string or list
     #
@@ -163,19 +173,24 @@ module T2Server
     # :call-seq:
     #   run.expiry -> string
     #
-    # Return the expiry time of this run. It is formatted as an ISO-8601
-    # timestamp.
+    # Return the expiry time of this run as an instance of class Time.
     def expiry
-      @server.get_run_attribute(@uuid, @links[:expiry])
+      Time.parse(@server.get_run_attribute(@uuid, @links[:expiry]))
     end
 
     # :call-seq:
     #   run.expiry=(time) -> bool
     #
     # Set the expiry time of this run to _time_. The format of _time_ should
-    # be an ISO-8601 timestamp.
-    def expiry=(date)
-      @server.set_run_attribute(@uuid, @links[:expiry], date)
+    # be something that the Ruby Time class can parse. If the value given does
+    # not specify a date then today's date will be assumed. If a time/date in
+    # the past is specified, the expiry time will not be changed.
+    def expiry=(time)
+      # need to massage the xmlschema format slightly as the server cannot
+      # parse timezone offsets with a colon (eg +00:00)
+      date_str = Time.parse(time).xmlschema(2)
+      date_str = date_str[0..-4] + date_str[-2..-1]
+      @server.set_run_attribute(@uuid, @links[:expiry], date_str)
     end
 
     # :call-seq:
@@ -363,44 +378,6 @@ module T2Server
       @server.get_run_attribute(@uuid, "#{@links[:wdir]}/#{@baclava_out}")
     end
 
-    # :call-seq:
-    #   run.ls(dir="") -> [[dirs], [objects]]
-    #
-    # List a directory in the run's workspace on the server. If _dir_ is left
-    # blank then / is listed. As there is no concept of changing into a
-    # directory (_cd_) in Taverna Server then all paths passed into _ls_
-    # should be full paths starting at "root". The contents of a directory are
-    # returned as a list of two lists, "directories" and "objects"
-    # respectively. In the case of listing the contents of the "out"
-    # directory, the "directories" returned by _ls_ are actually output port
-    # names and their contents are the values held by these ports. If there
-    # are multiple values listed then that port represents a list. If there
-    # are further directories below a port name then it is a list of lists.
-    def ls(dir="")
-      dir.strip_path!
-      dir_list = @server.get_run_attribute(@uuid, "#{@links[:wdir]}/#{dir}")
-
-      # compile a list of directory entries stripping the
-      # directory name from the front of each filename
-      dirs = []
-      files = []
-
-      begin
-        doc = XML::Document.string(dir_list)
-
-        doc.find(XPaths::DIR, Namespaces::MAP).each {|e| dirs << e.content.split('/')[-1]}
-        doc.find(XPaths::FILE, Namespaces::MAP).each {|e| files << e.content.split('/')[-1]}
-      rescue XML::Error => xmle
-        # We expect to get a DOCUMENT_EMPTY error in some cases. All others
-        # should be re-raised.
-        if xmle.code != XML::Error::DOCUMENT_EMPTY
-          raise xmle
-        end
-      end
-
-      [dirs, files]
-    end
-
     # :call-seq:
     #   run.initialized? -> bool
     #
@@ -428,35 +405,81 @@ module T2Server
     # :call-seq:
     #   run.create_time -> string
     #
-    # Get the creation time of this run formatted as an ISO-8601 timestamp.
+    # Get the creation time of this run as an instance of class Time.
     def create_time
-      @server.get_run_attribute(@uuid, @links[:createtime])
+      Time.parse(@server.get_run_attribute(@uuid, @links[:createtime]))
     end
 
     # :call-seq:
     #   run.start_time -> string
     #
-    # Get the start time of this run formatted as an ISO-8601 timestamp.
+    # Get the start time of this run as an instance of class Time.
     def start_time
-      @server.get_run_attribute(@uuid, @links[:starttime])
+      Time.parse(@server.get_run_attribute(@uuid, @links[:starttime]))
     end
 
     # :call-seq:
     #   run.finish_time -> string
     #
-    # Get the finish time of this run formatted as an ISO-8601 timestamp.
+    # Get the finish time of this run as an instance of class Time.
     def finish_time
-      @server.get_run_attribute(@uuid, @links[:finishtime])
+      Time.parse(@server.get_run_attribute(@uuid, @links[:finishtime]))
     end
 
     private
+
+    # List a directory in the run's workspace on the server. If dir is left
+    # blank then / is listed. As there is no concept of changing into a
+    # directory (cd) in Taverna Server then all paths passed into _ls_ports
+    # should be full paths starting at "root". The contents of a directory are
+    # returned as a list of two lists, "lists" and "values" respectively.
+    def _ls_ports(dir="", top=true)
+      dir.strip_path!
+      dir_list = @server.get_run_attribute(@uuid, "#{@links[:wdir]}/#{dir}")
+
+      # compile a list of directory entries stripping the
+      # directory name from the front of each filename
+      lists = []
+      values = []
+
+      begin
+        doc = XML::Document.string(dir_list)
+
+        doc.find(XPaths::DIR, Namespaces::MAP).each do |e|
+          if top
+            lists << e.content.split('/')[-1]
+          else
+            index = (e.attributes['name'].to_i - 1)
+            lists[index] = e.content.split('/')[-1]
+          end
+        end
+
+        doc.find(XPaths::FILE, Namespaces::MAP).each do |e|
+          if top
+            values << e.content.split('/')[-1]
+          else
+            index = (e.attributes['name'].to_i - 1)
+            values[index] = e.content.split('/')[-1]
+          end
+        end
+      rescue XML::Error => xmle
+        # We expect to get a DOCUMENT_EMPTY error in some cases. All others
+        # should be re-raised.
+        if xmle.code != XML::Error::DOCUMENT_EMPTY
+          raise xmle
+        end
+      end
+
+      [lists, values]
+    end
+
     def _get_output(output, refs=false, top=true)
       output.strip_path!
 
       # if at the top level we need to check if the port represents a list
       # or a singleton value
       if top
-        lists, items = ls("out")
+        lists, items = _ls_ports("out")
         if items.include? output
           if refs
             return "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}"
@@ -467,7 +490,7 @@ module T2Server
       end
 
       # we're not at the top level so look at the contents of the output port
-      lists, items = ls("out/#{output}")
+      lists, items = _ls_ports("out/#{output}", false)
 
       # build up lists of results
       result = []

data/lib/t2-server/server.rb

@@ -79,7 +79,9 @@ module T2Server
         @http.verify_mode = OpenSSL::SSL::VERIFY_NONE
       end
 
-      @links = parse_description(get_attribute(@rest_path))
+      # add a slash to the end of this address to work around this bug:
+      # http://www.mygrid.org.uk/dev/issues/browse/TAVSERV-113
+      @links = parse_description(get_attribute("#{@rest_path}/"))
       #@links.each {|key, val| puts "#{key}: #{val}"}
       
       # get max runs

data/lib/t2-server.rb

@@ -43,7 +43,7 @@ require 't2-server/run'
 #   Taverna 2 Server instance.
 module T2Server
   # The version of this library
-  GEM_VERSION = "0.5.3"
+  GEM_VERSION = "0.6.0"
   # The version of the Taverna 2 Server API that this library can interface with
   API_VERSION = "2.2a1"
 end

data/test/tc_run.rb

@@ -37,7 +37,7 @@ class TestRun < Test::Unit::TestCase
   def test_run
     # connection
     assert_nothing_raised(T2Server::ConnectionError) do
-      @run = T2Server::Run.create($address, $wkf_hello)
+      @run = T2Server::Run.create($address, $wkf_pass)
     end
 
     # test bad state code
@@ -45,11 +45,13 @@ class TestRun < Test::Unit::TestCase
       @run.wait
     end
 
-    # test mkdir and ls
+    # test mkdir
     assert(@run.mkdir("test"))
-    assert_equal(@run.ls, [["test"], []])
 
-    # start, state and wait
+    # set input, start, check state and wait
+    assert_nothing_raised(T2Server::AttributeNotFoundError) do
+      @run.set_input("IN", "Hello, World!")
+    end
     @run.start
     assert(@run.running?)
     assert_nothing_raised(T2Server::RunStateError) do
@@ -58,7 +60,7 @@ class TestRun < Test::Unit::TestCase
 
     # exitcode and output
     assert_instance_of(Fixnum, @run.exitcode)
-    assert_equal(@run.get_output("Message"), "Hello, World!")
+    assert_equal(@run.get_output("OUT"), "Hello, World!")
     assert_raise(T2Server::AccessForbiddenError) do
       @run.get_output("wrong!")
     end
@@ -66,11 +68,11 @@ class TestRun < Test::Unit::TestCase
     # deletion
     assert(@run.delete)
 
-    # run that need inputs
-    @run = T2Server::Run.create($address, $wkf_input)
+    # run with file input
+    @run = T2Server::Run.create($address, $wkf_pass)
 
     assert_nothing_raised(T2Server::AttributeNotFoundError) do
-      @run.set_input("input", 10)
+      @run.upload_input_file("IN", $file_input)
     end
 
     @run.start
@@ -78,6 +80,7 @@ class TestRun < Test::Unit::TestCase
     assert_nothing_raised(T2Server::RunStateError) do
       @run.wait
     end
+    assert_equal(@run.get_output("OUT"), "Hello, World!")
 
     # run that returns list of lists, some empty, using baclava for input
     @run = T2Server::Run.create($address, $wkf_lists)
@@ -90,13 +93,14 @@ class TestRun < Test::Unit::TestCase
     assert_nothing_raised(T2Server::RunStateError) do
       @run.wait
     end
+    assert_equal(@run.get_output_ports, ["SINGLE", "MANY"])
     assert_equal(@run.get_output("SINGLE"), [])
-    assert_equal(@run.get_output("MANY"), [[], [["Hello", ""]], [[], ["test"],
-      []], [["boo"]]])
+    assert_equal(@run.get_output("MANY"),
+      [[["boo"]], [["", "Hello"]], [], [[], ["test"], []]])
 
     # run with baclava output
-    @run = T2Server::Run.create($address, $wkf_hello)
-
+    @run = T2Server::Run.create($address, $wkf_pass)
+    @run.set_input("IN", "Some input...")
     assert_nothing_raised(T2Server::AttributeNotFoundError) do
       @run.set_baclava_output
     end

data/test/tc_server.rb

@@ -43,7 +43,7 @@ class TestServer < Test::Unit::TestCase
 
     # run creation
     assert_nothing_raised(T2Server::T2ServerError) do
-      @run = @server.create_run($wkf_hello)
+      @run = @server.create_run($wkf_pass)
     end
 
     # capacity
@@ -51,7 +51,7 @@ class TestServer < Test::Unit::TestCase
     assert_instance_of(Fixnum, limit)
     assert_raise(T2Server::ServerAtCapacityError) do
       limit.times do
-        @server.create_run($wkf_hello)
+        @server.create_run($wkf_pass)
       end
     end
   

data/test/ts_t2server.rb

@@ -33,26 +33,32 @@
 require 'test/unit'
 require 't2-server'
 
-# get a server address to test - 30 second timeout
-print "\nPlease supply a valid Taverna 2 Server address.\n\nNOTE that these " +
-  "tests will fully load the server and then delete all the runs that it " +
-  "has permission to do so - if you are not using security ALL runs will be " +
-  "deleted!\n(leave blank to skip tests): "
-$stdout.flush
-if select([$stdin], [], [], 30)
-  $address = $stdin.gets.chomp
+# check for a server address passed through on the command line
+if ARGV.size != 0:
+  $address = ARGV[0]
+  puts "Using server at #{$address}"
 else
-  puts "\nSkipping tests that require a Taverna 2 Server instance..."
-  $address = ""
+  # get a server address to test - 30 second timeout
+  print "\nPlease supply a valid Taverna 2 Server address.\n\nNOTE that " +
+    "these tests will fully load the server and then delete all the runs " +
+    "that it has permission to do so - if you are not using security ALL " +
+    "runs will be deleted!\n(leave blank to skip tests): "
+  $stdout.flush
+  if select([$stdin], [], [], 30)
+    $address = $stdin.gets.chomp
+  else
+    puts "\nSkipping tests that require a Taverna 2 Server instance..."
+    $address = ""
+  end
 end
 
 # the testcases to run
 require 'tc_paths'
 if $address != ""
-  $wkf_hello  = File.read("test/workflows/hello.t2flow")
-  $wkf_input  = File.read("test/workflows/pipelined_list_iteration_902021.t2flow")
+  $wkf_pass   = File.read("test/workflows/pass_through.t2flow")
   $wkf_lists  = File.read("test/workflows/empty_list.t2flow")
   $list_input = "test/workflows/empty_list_input.baclava"
+  $file_input = "test/workflows/in.txt"
 
   require 'tc_server'
   require 'tc_run'

data/test/workflows/empty_list.t2flow

@@ -1,23 +1,23 @@
-<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="">
-  <annotationAssertions>
-    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
-        <identification>536f469a-fd80-4efa-8d76-6cb2514123ec</identification>
-      </annotationBean>
-      <date>2010-11-04 18:00:12.867 GMT</date>
-      <creators />
-      <curationEventList />
-    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-  </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
-  <annotationAssertions>
-    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
-        <identification>373bb615-7dd3-46b4-9e3c-ee38e7460403</identification>
-      </annotationBean>
-      <date>2010-11-09 13:50:13.127 GMT</date>
-      <creators />
-      <curationEventList />
-    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-  </annotationAssertions>
+<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="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>536f469a-fd80-4efa-8d76-6cb2514123ec</identification>
+      </annotationBean>
+      <date>2010-11-04 18:00:12.867 GMT</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>373bb615-7dd3-46b4-9e3c-ee38e7460403</identification>
+      </annotationBean>
+      <date>2010-11-09 13:50:13.127 GMT</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
 </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>

data/test/workflows/empty_list_input.baclava

@@ -1,86 +1,86 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
-  <b:dataThing key="MANY_IN">
-    <b:myGridDataDocument lsid="" syntactictype="l(l(l('null')))">
-      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
-      <b:partialOrder lsid="" type="list">
-        <b:relationList>
-          <b:relation parent="0" child="1" />
-          <b:relation parent="1" child="2" />
-          <b:relation parent="2" child="3" />
-        </b:relationList>
-        <b:itemList>
-          <b:partialOrder lsid="" type="list" index="0">
-            <b:relationList />
-            <b:itemList>
-              <b:partialOrder lsid="" type="list" index="0">
-                <b:relationList />
-                <b:itemList>
-                  <b:dataElement lsid="" index="0">
-                    <b:dataElementData>Ym9v</b:dataElementData>
-                  </b:dataElement>
-                </b:itemList>
-              </b:partialOrder>
-            </b:itemList>
-          </b:partialOrder>
-          <b:partialOrder lsid="" type="list" index="1">
-            <b:relationList />
-            <b:itemList>
-              <b:partialOrder lsid="" type="list" index="0">
-                <b:relationList>
-                  <b:relation parent="0" child="1" />
-                </b:relationList>
-                <b:itemList>
-                  <b:dataElement lsid="" index="0">
-                    <b:dataElementData />
-                  </b:dataElement>
-                  <b:dataElement lsid="" index="1">
-                    <b:dataElementData>SGVsbG8=</b:dataElementData>
-                  </b:dataElement>
-                </b:itemList>
-              </b:partialOrder>
-            </b:itemList>
-          </b:partialOrder>
-          <b:partialOrder lsid="" type="list" index="2">
-            <b:relationList />
-            <b:itemList />
-          </b:partialOrder>
-          <b:partialOrder lsid="" type="list" index="3">
-            <b:relationList>
-              <b:relation parent="0" child="1" />
-              <b:relation parent="1" child="2" />
-            </b:relationList>
-            <b:itemList>
-              <b:partialOrder lsid="" type="list" index="0">
-                <b:relationList />
-                <b:itemList />
-              </b:partialOrder>
-              <b:partialOrder lsid="" type="list" index="1">
-                <b:relationList />
-                <b:itemList>
-                  <b:dataElement lsid="" index="0">
-                    <b:dataElementData>dGVzdA==</b:dataElementData>
-                  </b:dataElement>
-                </b:itemList>
-              </b:partialOrder>
-              <b:partialOrder lsid="" type="list" index="2">
-                <b:relationList />
-                <b:itemList />
-              </b:partialOrder>
-            </b:itemList>
-          </b:partialOrder>
-        </b:itemList>
-      </b:partialOrder>
-    </b:myGridDataDocument>
-  </b:dataThing>
-  <b:dataThing key="SINGLE_IN">
-    <b:myGridDataDocument lsid="" syntactictype="l('null')">
-      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
-      <b:partialOrder lsid="" type="list">
-        <b:relationList />
-        <b:itemList />
-      </b:partialOrder>
-    </b:myGridDataDocument>
-  </b:dataThing>
-</b:dataThingMap>
-
+<?xml version="1.0" encoding="UTF-8"?>
+<b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
+  <b:dataThing key="MANY_IN">
+    <b:myGridDataDocument lsid="" syntactictype="l(l(l('null')))">
+      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
+      <b:partialOrder lsid="" type="list">
+        <b:relationList>
+          <b:relation parent="0" child="1" />
+          <b:relation parent="1" child="2" />
+          <b:relation parent="2" child="3" />
+        </b:relationList>
+        <b:itemList>
+          <b:partialOrder lsid="" type="list" index="0">
+            <b:relationList />
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList />
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData>Ym9v</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="1">
+            <b:relationList />
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList>
+                  <b:relation parent="0" child="1" />
+                </b:relationList>
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData />
+                  </b:dataElement>
+                  <b:dataElement lsid="" index="1">
+                    <b:dataElementData>SGVsbG8=</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="2">
+            <b:relationList />
+            <b:itemList />
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="3">
+            <b:relationList>
+              <b:relation parent="0" child="1" />
+              <b:relation parent="1" child="2" />
+            </b:relationList>
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList />
+                <b:itemList />
+              </b:partialOrder>
+              <b:partialOrder lsid="" type="list" index="1">
+                <b:relationList />
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData>dGVzdA==</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+              <b:partialOrder lsid="" type="list" index="2">
+                <b:relationList />
+                <b:itemList />
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+        </b:itemList>
+      </b:partialOrder>
+    </b:myGridDataDocument>
+  </b:dataThing>
+  <b:dataThing key="SINGLE_IN">
+    <b:myGridDataDocument lsid="" syntactictype="l('null')">
+      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
+      <b:partialOrder lsid="" type="list">
+        <b:relationList />
+        <b:itemList />
+      </b:partialOrder>
+    </b:myGridDataDocument>
+  </b:dataThing>
+</b:dataThingMap>
+

data/test/workflows/in.txt

@@ -0,0 +1 @@
+Hello, World!

data/test/workflows/pass_through.t2flow

@@ -0,0 +1,12 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="b14e490b-927b-4e5e-9bb5-6c9b3da4ab2c" role="top"><name>Workflow1</name><inputPorts><port><name>IN</name><depth>0</depth><granularDepth>0</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="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>b14e490b-927b-4e5e-9bb5-6c9b3da4ab2c</identification>
+      </annotationBean>
+      <date>2010-11-22 13:37:10.158 GMT</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: t2-server
 version: !ruby/object:Gem::Version 
-  hash: 13
+  hash: 7
   prerelease: false
   segments: 
   - 0
-  - 5
-  - 3
-  version: 0.5.3
+  - 6
+  - 0
+  version: 0.6.0
 platform: ruby
 authors: 
 - Robert Haines
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-11-09 00:00:00 +00:00
+date: 2011-03-10 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -50,6 +50,22 @@ dependencies:
         version: 1.1.4
   type: :runtime
   version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: hirb
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 15
+        segments: 
+        - 0
+        - 4
+        - 0
+        version: 0.4.0
+  type: :runtime
+  version_requirements: *id003
 description: This gem provides access to the Taverna 2 Server REST interface from Ruby.
 email: rhaines@manchester.ac.uk
 executables: 
@@ -75,10 +91,10 @@ files:
 - test/tc_server.rb
 - test/tc_paths.rb
 - test/tc_run.rb
-- test/workflows/pipelined_list_iteration_902021.t2flow
+- test/workflows/pass_through.t2flow
 - test/workflows/empty_list_input.baclava
 - test/workflows/empty_list.t2flow
-- test/workflows/hello.t2flow
+- test/workflows/in.txt
 - test/ts_t2server.rb
 - README.rdoc
 - LICENCE.rdoc

data/test/workflows/hello.t2flow

@@ -1,21 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="b9556b39-8656-4a17-bf5c-37de30fe7df3" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>Message</name><annotations /></port></outputPorts><processors><processor><name>Hello</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="">
-  <value>Hello, World!</value>
-</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="">
-  <maxJobs>1</maxJobs>
-</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="">
-  <backoffFactor>1.0</backoffFactor>
-  <initialDelay>1000</initialDelay>
-  <maxDelay>5000</maxDelay>
-  <maxRetries>0</maxRetries>
-</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 /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>Message</port></sink><source type="processor"><processor>Hello</processor><port>value</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
-  <annotationAssertions>
-    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
-        <identification>b9556b39-8656-4a17-bf5c-37de30fe7df3</identification>
-      </annotationBean>
-      <date>2010-07-09 15:01:39.283 BST</date>
-      <creators />
-      <curationEventList />
-    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-  </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>

data/test/workflows/pipelined_list_iteration_902021.t2flow

@@ -1,303 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="fd34324d-de34-4a5f-9b12-13059a9fb1a4" role="top"><name>Pipelined_list_iteration</name><inputPorts><port><name>input</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
-  <annotationAssertions>
-    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
-        <text>150</text>
-      </annotationBean>
-      <date>2009-12-15 19:41:02.598 GMT</date>
-      <creators />
-      <curationEventList />
-    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-  </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
-  <annotationAssertions>
-    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
-        <text>Number of elements to generate</text>
-      </annotationBean>
-      <date>2009-12-15 19:40:52.84 GMT</date>
-      <creators />
-      <curationEventList />
-    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-  </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>List_Emitter</name><inputPorts><port><name>count</name><depth>0</depth></port></inputPorts><outputPorts><port><name>list</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="count" to="count" /></inputMap><outputMap><map from="list" to="list" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
-  <script>List list = new ArrayList();
-int icount = Integer.parseInt(count);
-
-for (int i=0;i&lt;icount;i++) {
-	list.add(String.valueOf(i));
-}</script>
-  <dependencies />
-  <classLoaderSharing>workflow</classLoaderSharing>
-  <localDependencies />
-  <artifactDependencies />
-  <inputs>
-    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
-      <handledReferenceSchemes />
-      <translatedElementType>java.lang.String</translatedElementType>
-      <allowsLiteralValues>true</allowsLiteralValues>
-      <name>count</name>
-      <depth>0</depth>
-      <mimeTypes>
-        <string>text/plain</string>
-      </mimeTypes>
-    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
-  </inputs>
-  <outputs>
-    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
-      <granularDepth>1</granularDepth>
-      <name>list</name>
-      <depth>1</depth>
-      <mimeTypes />
-    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
-  </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">
-  <maxJobs>1</maxJobs>
-</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="">
-  <backoffFactor>1.0</backoffFactor>
-  <initialDelay>1000</initialDelay>
-  <maxDelay>5000</maxDelay>
-  <maxRetries>0</maxRetries>
-</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="count" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concat</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
-  <script>String output = input + "XXX"</script>
-  <dependencies />
-  <classLoaderSharing>workflow</classLoaderSharing>
-  <localDependencies />
-  <artifactDependencies />
-  <inputs>
-    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
-      <handledReferenceSchemes />
-      <translatedElementType>java.lang.String</translatedElementType>
-      <allowsLiteralValues>true</allowsLiteralValues>
-      <name>input</name>
-      <depth>0</depth>
-      <mimeTypes>
-        <string>text/plain</string>
-      </mimeTypes>
-    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
-  </inputs>
-  <outputs>
-    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
-      <granularDepth>0</granularDepth>
-      <name>output</name>
-      <depth>0</depth>
-      <mimeTypes />
-    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
-  </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">
-  <maxJobs>1</maxJobs>
-</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="">
-  <backoffFactor>1.0</backoffFactor>
-  <initialDelay>1000</initialDelay>
-  <maxDelay>5000</maxDelay>
-  <maxRetries>0</maxRetries>
-</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="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string1</name><depth>0</depth></port><port><name>string2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</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="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
-  <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
-  <script>output = string1 + string2;</script>
-  <dependencies />
-  <classLoaderSharing>workflow</classLoaderSharing>
-  <localDependencies />
-  <artifactDependencies />
-  <inputs>
-    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
-      <handledReferenceSchemes />
-      <translatedElementType>java.lang.String</translatedElementType>
-      <allowsLiteralValues>true</allowsLiteralValues>
-      <name>string1</name>
-      <depth>0</depth>
-      <mimeTypes>
-        <string>'text/plain'</string>
-      </mimeTypes>
-    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
-    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
-      <handledReferenceSchemes />
-      <translatedElementType>java.lang.String</translatedElementType>
-      <allowsLiteralValues>true</allowsLiteralValues>
-      <name>string2</name>
-      <depth>0</depth>
-      <mimeTypes>
-        <string>'text/plain'</string>
-      </mimeTypes>
-    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
-  </inputs>
-  <outputs>
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-      <date>2009-12-15 19:42:21.971 GMT</date>
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-        <text>Ian Dunlop, Stian Soiland-Reyes</text>
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-      <date>2009-12-15 19:42:01.488 GMT</date>
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-      <date>2010-07-04 18:19:17.425 BST</date>
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