t2-server 0.5.1 → 0.5.2

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Files changed (11) hide show
  1. data/CHANGES.rdoc +5 -0
  2. data/README.rdoc +1 -1
  3. data/lib/t2-server.rb +1 -1
  4. data/lib/t2-server/run.rb +42 -35
  5. data/test/tc_run.rb +10 -11
  6. data/test/ts_t2server.rb +2 -2
  7. data/test/workflows/empty_list.t2flow +12 -0
  8. data/test/workflows/empty_list_input.baclava +77 -0
  9. metadata +6 -6
  10. data/test/workflows/demonstration_of_configurable_iteration_114130.t2flow +0 -335
  11. data/test/workflows/list_input.baclava +0 -16
data/CHANGES.rdoc CHANGED
@@ -1,5 +1,10 @@
1
1
  = Changes log for the T2 Ruby Gem
2
2
 
3
+ == Version 0.5.2
4
+
5
+ * Fix two issues with the retrieving of workflow outputs.
6
+ * Update tests to reflect changes to output code.
7
+
3
8
  == Version 0.5.1
4
9
 
5
10
  * Fix horror typo in Server#set_run_input.
data/README.rdoc CHANGED
@@ -1,7 +1,7 @@
1
1
  = Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem
2
2
 
3
3
  Authors:: Robert Haines
4
- Gem Version:: 0.5.1
4
+ Gem Version:: 0.5.2
5
5
  API Version:: 2.2a1
6
6
  Contact:: mailto:rhaines@manchester.ac.uk
7
7
  URL:: http://taverna.sourceforge.net/
data/lib/t2-server.rb CHANGED
@@ -43,7 +43,7 @@ require 't2-server/run'
43
43
  # Taverna 2 Server instance.
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44
  module T2Server
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45
  # The version of this library
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- GEM_VERSION = "0.5.1"
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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
data/lib/t2-server/run.rb CHANGED
@@ -137,53 +137,27 @@ module T2Server
137
137
  end
138
138
 
139
139
  # :call-seq:
140
- # run.get_output(output, refs=false) -> list
140
+ # run.get_output(output, refs=false) -> string or list
141
141
  #
142
142
  # Return the values of the workflow output port _output_. These are
143
- # returned as a list of strings. If the output port represents a singleton
144
- # output then a one item list is returned. By default this method returns
143
+ # returned as a list of strings or, if the output port represents a
144
+ # singleton value, then a string returned. By default this method returns
145
145
  # the actual data from the output port but if _refs_ is set to true then
146
146
  # it will instead return URIs to the actual data in the same list format.
147
147
  # See also Run#get_output_refs.
148
148
  def get_output(output, refs=false)
149
- output.strip_path!
150
- result = []
151
-
152
- # look at the contents of the output port
153
- lists, items = ls("out/#{output}")
154
-
155
- # if lists and items are empty then it's a single value
156
- if lists == [] and items == []
157
- if refs
158
- result << "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}"
159
- else
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- result << @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}")
161
- end
162
- end
163
-
164
- # for each list recurse into it and add the items to the result
165
- lists.each {|list| result << get_output("#{output}/#{list}", refs)}
166
-
167
- # for each item, add it to the output list
168
- items.each do |item|
169
- if refs
170
- result << "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}/#{item}"
171
- else
172
- result << @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}/#{item}")
173
- end
174
- end
175
-
176
- result
149
+ _get_output(output, refs)
177
150
  end
178
151
 
179
152
  # :call-seq:
180
- # run.get_output_refs(output) -> list
153
+ # run.get_output_refs(output) -> string or list
181
154
  #
182
155
  # Return references (URIs) to the values of the workflow output port
183
- # _output_. These are returned as a list of URIs. If the output port
184
- # represents a singleton output then a one item list is returned.
156
+ # _output_. These are returned as a list of URIs or, if the output port
157
+ # represents a singleton value, then a single URI is returned. The URIs
158
+ # are returned as strings.
185
159
  def get_output_refs(output)
186
- get_output(output, true)
160
+ _get_output(output, true)
187
161
  end
188
162
 
189
163
  # :call-seq:
@@ -476,6 +450,39 @@ module T2Server
476
450
  end
477
451
 
478
452
  private
453
+ def _get_output(output, refs=false, top=true)
454
+ output.strip_path!
455
+ result = []
456
+
457
+ # look at the contents of the output port
458
+ lists, items = ls("out/#{output}")
459
+
460
+ # if lists and items are empty then it's an empty list
461
+ # although it could be a single value if we're at the top level
462
+ if top and lists == [] and items == []
463
+ # as we are at the top level, just return the single value
464
+ if refs
465
+ return "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}"
466
+ else
467
+ return @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}")
468
+ end
469
+ end
470
+
471
+ # for each list recurse into it and add the items to the result
472
+ lists.each {|list| result << _get_output("#{output}/#{list}", refs, false)}
473
+
474
+ # for each item, add it to the output list
475
+ items.each do |item|
476
+ if refs
477
+ result << "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}/#{item}"
478
+ else
479
+ result << @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}/#{item}")
480
+ end
481
+ end
482
+
483
+ result
484
+ end
485
+
479
486
  def get_attributes(desc)
480
487
  # first parse out the basic stuff
481
488
  links = parse_description(desc)
data/test/tc_run.rb CHANGED
@@ -58,7 +58,7 @@ class TestRun < Test::Unit::TestCase
58
58
 
59
59
  # exitcode and output
60
60
  assert_instance_of(Fixnum, @run.exitcode)
61
- assert_equal(@run.get_output("Message"), ["Hello, World!"])
61
+ assert_equal(@run.get_output("Message"), "Hello, World!")
62
62
  assert_raise(T2Server::AccessForbiddenError) do
63
63
  @run.get_output("wrong!")
64
64
  end
@@ -79,24 +79,23 @@ class TestRun < Test::Unit::TestCase
79
79
  @run.wait
80
80
  end
81
81
 
82
- # run that returns list of lists
82
+ # run that returns list of lists, some empty, using baclava for input
83
83
  @run = T2Server::Run.create($address, $wkf_lists)
84
+ assert_nothing_raised(T2Server::AttributeNotFoundError) do
85
+ @run.upload_baclava_file($list_input)
86
+ end
87
+
84
88
  @run.start
85
89
  assert(@run.running?)
86
90
  assert_nothing_raised(T2Server::RunStateError) do
87
91
  @run.wait
88
92
  end
89
- assert_equal(@run.get_output("Output"), [["triangular green rabbit ",
90
- "triangular red cat "], ["circular green rabbit ", "circular red cat "],
91
- ["square green rabbit ", "square red cat "]])
93
+ assert_equal(@run.get_output("OUT"), [[["boo"]], [["", "hello"]],
94
+ [], [[], ["test"], []]])
92
95
 
93
- # run with baclava input and output
94
- @run = T2Server::Run.create($address, $wkf_input)
96
+ # run with baclava output
97
+ @run = T2Server::Run.create($address, $wkf_hello)
95
98
 
96
- assert_nothing_raised(T2Server::AttributeNotFoundError) do
97
- @run.upload_baclava_file($baclava_in)
98
- end
99
-
100
99
  assert_nothing_raised(T2Server::AttributeNotFoundError) do
101
100
  @run.set_baclava_output
102
101
  end
data/test/ts_t2server.rb CHANGED
@@ -51,8 +51,8 @@ require 'tc_paths'
51
51
  if $address != ""
52
52
  $wkf_hello = File.read("test/workflows/hello.t2flow")
53
53
  $wkf_input = File.read("test/workflows/pipelined_list_iteration_902021.t2flow")
54
- $wkf_lists = File.read("test/workflows/demonstration_of_configurable_iteration_114130.t2flow")
55
- $baclava_in = "test/workflows/list_input.baclava"
54
+ $wkf_lists = File.read("test/workflows/empty_list.t2flow")
55
+ $list_input = "test/workflows/empty_list_input.baclava"
56
56
 
57
57
  require 'tc_server'
58
58
  require 'tc_run'
data/test/workflows/empty_list.t2flow ADDED
@@ -0,0 +1,12 @@
1
+ <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="">
2
+ <annotationAssertions>
3
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
4
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
5
+ <identification>536f469a-fd80-4efa-8d76-6cb2514123ec</identification>
6
+ </annotationBean>
7
+ <date>2010-11-04 18:00:12.867 GMT</date>
8
+ <creators />
9
+ <curationEventList />
10
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
11
+ </annotationAssertions>
12
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
data/test/workflows/empty_list_input.baclava ADDED
@@ -0,0 +1,77 @@
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
3
+ <b:dataThing key="IN">
4
+ <b:myGridDataDocument lsid="" syntactictype="l(l('null'))">
5
+ <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
6
+ <b:partialOrder lsid="" type="list">
7
+ <b:relationList>
8
+ <b:relation parent="0" child="1" />
9
+ <b:relation parent="1" child="2" />
10
+ <b:relation parent="2" child="3" />
11
+ </b:relationList>
12
+ <b:itemList>
13
+ <b:partialOrder lsid="" type="list" index="0">
14
+ <b:relationList>
15
+ <b:relation parent="0" child="1" />
16
+ <b:relation parent="1" child="2" />
17
+ </b:relationList>
18
+ <b:itemList>
19
+ <b:partialOrder lsid="" type="list" index="0">
20
+ <b:relationList />
21
+ <b:itemList />
22
+ </b:partialOrder>
23
+ <b:partialOrder lsid="" type="list" index="1">
24
+ <b:relationList />
25
+ <b:itemList>
26
+ <b:dataElement lsid="" index="0">
27
+ <b:dataElementData>dGVzdA==</b:dataElementData>
28
+ </b:dataElement>
29
+ </b:itemList>
30
+ </b:partialOrder>
31
+ <b:partialOrder lsid="" type="list" index="2">
32
+ <b:relationList />
33
+ <b:itemList />
34
+ </b:partialOrder>
35
+ </b:itemList>
36
+ </b:partialOrder>
37
+ <b:partialOrder lsid="" type="list" index="1">
38
+ <b:relationList />
39
+ <b:itemList>
40
+ <b:partialOrder lsid="" type="list" index="0">
41
+ <b:relationList>
42
+ <b:relation parent="0" child="1" />
43
+ </b:relationList>
44
+ <b:itemList>
45
+ <b:dataElement lsid="" index="0">
46
+ <b:dataElementData>aGVsbG8=</b:dataElementData>
47
+ </b:dataElement>
48
+ <b:dataElement lsid="" index="1">
49
+ <b:dataElementData />
50
+ </b:dataElement>
51
+ </b:itemList>
52
+ </b:partialOrder>
53
+ </b:itemList>
54
+ </b:partialOrder>
55
+ <b:partialOrder lsid="" type="list" index="2">
56
+ <b:relationList />
57
+ <b:itemList>
58
+ <b:partialOrder lsid="" type="list" index="0">
59
+ <b:relationList />
60
+ <b:itemList>
61
+ <b:dataElement lsid="" index="0">
62
+ <b:dataElementData>Ym9v</b:dataElementData>
63
+ </b:dataElement>
64
+ </b:itemList>
65
+ </b:partialOrder>
66
+ </b:itemList>
67
+ </b:partialOrder>
68
+ <b:partialOrder lsid="" type="list" index="3">
69
+ <b:relationList />
70
+ <b:itemList />
71
+ </b:partialOrder>
72
+ </b:itemList>
73
+ </b:partialOrder>
74
+ </b:myGridDataDocument>
75
+ </b:dataThing>
76
+ </b:dataThingMap>
77
+
metadata CHANGED
@@ -1,13 +1,13 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: t2-server
3
3
  version: !ruby/object:Gem::Version
4
- hash: 9
4
+ hash: 15
5
5
  prerelease: false
6
6
  segments:
7
7
  - 0
8
8
  - 5
9
- - 1
10
- version: 0.5.1
9
+ - 2
10
+ version: 0.5.2
11
11
  platform: ruby
12
12
  authors:
13
13
  - Robert Haines
@@ -15,7 +15,7 @@ autorequire:
15
15
  bindir: bin
16
16
  cert_chain: []
17
17
 
18
- date: 2010-10-29 00:00:00 +01:00
18
+ date: 2010-11-05 00:00:00 +00:00
19
19
  default_executable:
20
20
  dependencies:
21
21
  - !ruby/object:Gem::Dependency
@@ -75,9 +75,9 @@ files:
75
75
  - test/tc_server.rb
76
76
  - test/tc_paths.rb
77
77
  - test/tc_run.rb
78
- - test/workflows/list_input.baclava
79
78
  - test/workflows/pipelined_list_iteration_902021.t2flow
80
- - test/workflows/demonstration_of_configurable_iteration_114130.t2flow
79
+ - test/workflows/empty_list_input.baclava
80
+ - test/workflows/empty_list.t2flow
81
81
  - test/workflows/hello.t2flow
82
82
  - test/ts_t2server.rb
83
83
  - README.rdoc
data/test/workflows/demonstration_of_configurable_iteration_114130.t2flow DELETED
@@ -1,335 +0,0 @@
1
- <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="">
2
- <value>red ,green ,</value>
3
- </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="">
4
- <maxJobs>1</maxJobs>
5
- </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="">
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
- <value>cat ,rabbit ,</value>
12
- </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
- <maxJobs>1</maxJobs>
14
- </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
- <initialDelay>0</initialDelay>
17
- <maxDelay>0</maxDelay>
18
- <maxRetries>0</maxRetries>
19
- </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
- <value>square ,circular ,triangular ,</value>
21
- </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
- <maxJobs>1</maxJobs>
23
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25
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27
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28
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29
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
30
- <script>List split = new ArrayList();
31
- if (!string.equals("")) {
32
- String regexString = ",";
33
- if (regex != void) {
34
- regexString = regex;
35
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36
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37
- for (int i = 0; i &lt; result.length; i++) {
38
- split.add(result[i]);
39
- }
40
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41
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42
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43
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44
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45
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46
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47
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48
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50
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51
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52
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54
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55
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56
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57
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58
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59
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60
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61
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62
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63
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64
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65
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66
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67
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68
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69
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
70
- <granularDepth>1</granularDepth>
71
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72
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81
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82
- <initialDelay>1000</initialDelay>
83
- <maxDelay>5000</maxDelay>
84
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85
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- <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
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94
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95
- split.add(result[i]);
96
- }
97
- }
98
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99
- <dependencies />
100
- <classLoaderSharing>workflow</classLoaderSharing>
101
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102
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103
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104
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105
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106
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107
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108
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109
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112
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113
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114
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116
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117
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119
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122
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123
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124
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125
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126
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127
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128
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129
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132
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133
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134
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135
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136
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137
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138
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139
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140
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141
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142
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143
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144
- <script>List split = new ArrayList();
145
- if (!string.equals("")) {
146
- String regexString = ",";
147
- if (regex != void) {
148
- regexString = regex;
149
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150
- String[] result = string.split(regexString);
151
- for (int i = 0; i &lt; 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
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162
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163
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164
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165
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166
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167
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168
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169
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170
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171
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172
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173
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174
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175
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176
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179
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180
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181
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182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
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196
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197
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198
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199
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200
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201
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202
- <dependencies />
203
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204
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205
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206
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207
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208
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209
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210
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211
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212
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213
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214
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215
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216
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217
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218
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219
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220
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221
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222
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223
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224
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225
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226
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227
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228
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229
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230
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231
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232
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233
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234
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235
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236
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237
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238
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239
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240
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241
- <backoffFactor>1.0</backoffFactor>
242
- <initialDelay>1000</initialDelay>
243
- <maxDelay>5000</maxDelay>
244
- <maxRetries>0</maxRetries>
245
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246
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247
- <script>output = string1 + string2;</script>
248
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249
- <classLoaderSharing>workflow</classLoaderSharing>
250
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251
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252
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253
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254
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255
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256
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257
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258
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259
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260
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261
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262
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263
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264
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265
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266
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267
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268
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269
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270
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271
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272
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273
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274
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275
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276
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277
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278
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279
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280
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281
- </mimeTypes>
282
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
283
- </outputs>
284
- </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="">
285
- <maxJobs>1</maxJobs>
286
- </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="">
287
- <backoffFactor>1.0</backoffFactor>
288
- <initialDelay>1000</initialDelay>
289
- <maxDelay>5000</maxDelay>
290
- <maxRetries>0</maxRetries>
291
- </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="string1" depth="0" /><port name="string2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>ColoursLisr</processor><port>string</port></sink><source type="processor"><processor>Colours</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>AnimalsList</processor><port>string</port></sink><source type="processor"><processor>Animals</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>ShapesList</processor><port>string</port></sink><source type="processor"><processor>Shapes</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="processor"><processor>ColoursLisr</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="processor"><processor>AnimalsList</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>ShapeAnimals</processor><port>string2</port></sink><source type="processor"><processor>Concatenate_two_strings</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>ShapeAnimals</processor><port>string1</port></sink><source type="processor"><processor>ShapesList</processor><port>split</port></source></datalink><datalink><sink type="dataflow"><port>Output</port></sink><source type="processor"><processor>ShapeAnimals</processor><port>output</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
292
- <annotationAssertions>
293
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
294
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
295
- <text>This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.</text>
296
- </annotationBean>
297
- <date>2009-06-29 15:44:05.675 BST</date>
298
- <creators />
299
- <curationEventList />
300
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
301
- </annotationAssertions>
302
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
303
- <annotationAssertions>
304
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
305
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
306
- <text>Tom Oinn</text>
307
- </annotationBean>
308
- <date>2009-06-29 15:44:05.675 BST</date>
309
- <creators />
310
- <curationEventList />
311
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
312
- </annotationAssertions>
313
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
314
- <annotationAssertions>
315
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
316
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
317
- <identification>be152f54-e4a7-4324-9ce6-44438c5daed7</identification>
318
- </annotationBean>
319
- <date>2010-07-04 18:12:25.361 BST</date>
320
- <creators />
321
- <curationEventList />
322
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
323
- </annotationAssertions>
324
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
325
- <annotationAssertions>
326
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
327
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
328
- <text>Demonstration of configurable iteration</text>
329
- </annotationBean>
330
- <date>2009-06-29 15:44:05.675 BST</date>
331
- <creators />
332
- <curationEventList />
333
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
334
- </annotationAssertions>
335
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
data/test/workflows/list_input.baclava DELETED
@@ -1,16 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
2
- <b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
3
- <b:dataThing key="input">
4
- <b:myGridDataDocument lsid="" syntactictype="'text/plain'">
5
- <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">
6
- <s:mimeTypes>
7
- <s:mimeType>text/plain</s:mimeType>
8
- </s:mimeTypes>
9
- </s:metadata>
10
- <b:dataElement lsid="">
11
- <b:dataElementData>MTA=</b:dataElementData>
12
- </b:dataElement>
13
- </b:myGridDataDocument>
14
- </b:dataThing>
15
- </b:dataThingMap>
16
-