t2-server 0.9.3 → 1.0.0
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- data/CHANGES.rdoc +79 -0
- data/LICENCE.rdoc +1 -1
- data/README.rdoc +94 -26
- data/Rakefile +6 -5
- data/bin/t2-delete-runs +25 -23
- data/bin/t2-get-output +11 -13
- data/bin/t2-run-workflow +91 -29
- data/bin/t2-server-info +29 -12
- data/extras/t2-server-stress +184 -0
- data/lib/t2-server-cli.rb +48 -23
- data/lib/t2-server.rb +2 -1
- data/lib/t2-server/admin.rb +7 -4
- data/lib/t2-server/exceptions.rb +23 -4
- data/lib/t2-server/interaction.rb +241 -0
- data/lib/t2-server/net/connection.rb +90 -60
- data/lib/t2-server/net/credentials.rb +25 -9
- data/lib/t2-server/net/parameters.rb +21 -6
- data/lib/t2-server/port.rb +229 -140
- data/lib/t2-server/run-cache.rb +99 -0
- data/lib/t2-server/run.rb +349 -332
- data/lib/t2-server/server.rb +115 -164
- data/lib/t2-server/util.rb +11 -9
- data/lib/t2-server/xml/libxml.rb +3 -2
- data/lib/t2-server/xml/nokogiri.rb +4 -3
- data/lib/t2-server/xml/rexml.rb +3 -2
- data/lib/t2-server/xml/xml.rb +47 -36
- data/lib/{t2server.rb → t2-server/xml/xpath_cache.rb} +29 -7
- data/t2-server.gemspec +16 -5
- data/test/tc_misc.rb +61 -0
- data/test/tc_perms.rb +17 -1
- data/test/tc_run.rb +164 -34
- data/test/tc_secure.rb +11 -2
- data/test/tc_server.rb +23 -2
- data/test/ts_t2server.rb +10 -8
- data/test/workflows/missing_outputs.t2flow +440 -0
- data/version.yml +3 -3
- metadata +42 -4
data/test/tc_secure.rb
CHANGED
@@ -75,6 +75,7 @@ class TestSecurity < Test::Unit::TestCase
|
|
75
75
|
assert_nothing_raised(T2Server::RunStateError) { run.wait }
|
76
76
|
assert(run.finished?)
|
77
77
|
assert_not_nil(run.output_port("out").value)
|
78
|
+
assert(run.delete)
|
78
79
|
end
|
79
80
|
|
80
81
|
# now test with no credential
|
@@ -83,7 +84,8 @@ class TestSecurity < Test::Unit::TestCase
|
|
83
84
|
assert(run.running?)
|
84
85
|
assert_nothing_raised(T2Server::RunStateError) { run.wait }
|
85
86
|
assert(run.finished?)
|
86
|
-
|
87
|
+
assert(run.output_port("out").error?)
|
88
|
+
assert(run.delete)
|
87
89
|
end
|
88
90
|
end
|
89
91
|
|
@@ -97,6 +99,7 @@ class TestSecurity < Test::Unit::TestCase
|
|
97
99
|
assert_nothing_raised(T2Server::RunStateError) { run.wait }
|
98
100
|
assert(run.finished?)
|
99
101
|
assert_not_nil(run.output_port("out").value)
|
102
|
+
assert(run.delete)
|
100
103
|
end
|
101
104
|
|
102
105
|
# now test with no server public key
|
@@ -106,7 +109,8 @@ class TestSecurity < Test::Unit::TestCase
|
|
106
109
|
assert(run.running?)
|
107
110
|
assert_nothing_raised(T2Server::RunStateError) { run.wait }
|
108
111
|
assert(run.finished?)
|
109
|
-
|
112
|
+
assert(run.output_port("out").error?)
|
113
|
+
assert(run.delete)
|
110
114
|
end
|
111
115
|
end
|
112
116
|
|
@@ -119,6 +123,7 @@ class TestSecurity < Test::Unit::TestCase
|
|
119
123
|
assert_nothing_raised(T2Server::RunStateError) { run.wait }
|
120
124
|
assert(run.finished?)
|
121
125
|
assert_not_nil(run.output_port("out").value)
|
126
|
+
assert(run.delete)
|
122
127
|
end
|
123
128
|
end
|
124
129
|
|
@@ -132,6 +137,7 @@ class TestSecurity < Test::Unit::TestCase
|
|
132
137
|
assert_nothing_raised(T2Server::RunStateError) { run.wait }
|
133
138
|
assert(run.finished?)
|
134
139
|
assert_not_nil(run.output_port("out").value)
|
140
|
+
assert(run.delete)
|
135
141
|
end
|
136
142
|
end
|
137
143
|
|
@@ -152,6 +158,7 @@ class TestSecurity < Test::Unit::TestCase
|
|
152
158
|
"Hello Alex!")
|
153
159
|
assert_equal(run.output_port("out_digest_timestamp").value,
|
154
160
|
"Hello David!")
|
161
|
+
assert(run.delete)
|
155
162
|
end
|
156
163
|
end
|
157
164
|
|
@@ -173,6 +180,7 @@ class TestSecurity < Test::Unit::TestCase
|
|
173
180
|
"Hello Alex!")
|
174
181
|
assert_equal(run.output_port("out_digest_timestamp").value,
|
175
182
|
"Hello David!")
|
183
|
+
assert(run.delete)
|
176
184
|
end
|
177
185
|
end
|
178
186
|
|
@@ -186,6 +194,7 @@ class TestSecurity < Test::Unit::TestCase
|
|
186
194
|
assert_nothing_raised(T2Server::RunStateError) { run.wait }
|
187
195
|
assert(run.finished?)
|
188
196
|
assert_not_nil(run.output_port("out").value)
|
197
|
+
assert(run.delete)
|
189
198
|
end
|
190
199
|
end
|
191
200
|
end
|
data/test/tc_server.rb
CHANGED
@@ -1,4 +1,4 @@
|
|
1
|
-
# Copyright (c) 2010-
|
1
|
+
# Copyright (c) 2010-2013 The University of Manchester, UK.
|
2
2
|
#
|
3
3
|
# All rights reserved.
|
4
4
|
#
|
@@ -40,6 +40,12 @@ class TestServer < Test::Unit::TestCase
|
|
40
40
|
end
|
41
41
|
end
|
42
42
|
|
43
|
+
def test_server_connection_no_params
|
44
|
+
assert_nothing_raised(T2Server::ConnectionError) do
|
45
|
+
T2Server::Server.new($uri)
|
46
|
+
end
|
47
|
+
end
|
48
|
+
|
43
49
|
def test_run_creation
|
44
50
|
T2Server::Server.new($uri, $conn_params) do |server|
|
45
51
|
assert_nothing_raised(T2Server::T2ServerError) do
|
@@ -53,14 +59,29 @@ class TestServer < Test::Unit::TestCase
|
|
53
59
|
def test_server_limits_delete_all
|
54
60
|
T2Server::Server.new($uri, $conn_params) do |server|
|
55
61
|
limit = server.run_limit($creds)
|
62
|
+
max_runs = 0
|
56
63
|
assert_instance_of(Fixnum, limit)
|
57
64
|
assert_raise(T2Server::ServerAtCapacityError) do
|
65
|
+
# Detect the concurrent run limit and
|
58
66
|
# add 1 just in case there are no runs at this point
|
67
|
+
more = true
|
59
68
|
(limit + 1).times do
|
60
|
-
server.create_run($wkf_pass, $creds)
|
69
|
+
run = server.create_run($wkf_pass, $creds)
|
70
|
+
if more
|
71
|
+
run.input_port("IN").value = "Hello"
|
72
|
+
more = run.start
|
73
|
+
if more
|
74
|
+
max_runs += 1
|
75
|
+
assert(run.running?)
|
76
|
+
else
|
77
|
+
assert(run.initialized?)
|
78
|
+
end
|
79
|
+
end
|
61
80
|
end
|
62
81
|
end
|
63
82
|
|
83
|
+
assert(max_runs <= limit)
|
84
|
+
|
64
85
|
assert_nothing_raised(T2Server::T2ServerError) do
|
65
86
|
server.delete_all_runs($creds)
|
66
87
|
end
|
data/test/ts_t2server.rb
CHANGED
@@ -1,4 +1,4 @@
|
|
1
|
-
# Copyright (c) 2010-
|
1
|
+
# Copyright (c) 2010-2013 The University of Manchester, UK.
|
2
2
|
#
|
3
3
|
# All rights reserved.
|
4
4
|
#
|
@@ -78,13 +78,14 @@ if address != ""
|
|
78
78
|
$creds = T2Server::HttpBasic.new(user1, pass1) if user1
|
79
79
|
$creds1 = T2Server::HttpBasic.new(user2, pass2) if user2
|
80
80
|
|
81
|
-
$wkf_pass =
|
82
|
-
$wkf_lists =
|
83
|
-
$wkf_l_v =
|
84
|
-
$wkf_xml =
|
85
|
-
$wkf_fail =
|
86
|
-
$wkf_errors =
|
87
|
-
$wkf_no_io =
|
81
|
+
$wkf_pass = "test/workflows/pass_through.t2flow"
|
82
|
+
$wkf_lists = "test/workflows/empty_list.t2flow"
|
83
|
+
$wkf_l_v = "test/workflows/list_and_value.t2flow"
|
84
|
+
$wkf_xml = "test/workflows/xml_xpath.t2flow"
|
85
|
+
$wkf_fail = "test/workflows/always_fail.t2flow"
|
86
|
+
$wkf_errors = "test/workflows/list_with_errors.t2flow"
|
87
|
+
$wkf_no_io = "test/workflows/no-ports.t2flow"
|
88
|
+
$wkf_miss_o = "test/workflows/missing_outputs.t2flow"
|
88
89
|
$list_input = "test/workflows/empty_list_input.baclava"
|
89
90
|
$file_input = "test/workflows/in.txt"
|
90
91
|
$file_strs = "test/workflows/strings.txt"
|
@@ -104,6 +105,7 @@ if address != ""
|
|
104
105
|
require 'tc_run'
|
105
106
|
require 'tc_admin'
|
106
107
|
require 'tc_secure'
|
108
|
+
require 'tc_misc'
|
107
109
|
|
108
110
|
# if we have two sets of credentials we can run permissions tests
|
109
111
|
if $creds1
|
@@ -0,0 +1,440 @@
|
|
1
|
+
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="7cc6cd61-0e6a-48ee-936c-9123b2ac3faf" role="top"><name>Workflow4</name><inputPorts /><outputPorts><port><name>OUT_1</name><annotations /></port><port><name>OUT_2</name><annotations /></port><port><name>OUT_3</name><annotations /></port></outputPorts><processors><processor><name>Passthrough_1</name><inputPorts><port><name>in1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out1</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>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in1" to="in1" /></inputMap><outputMap><map from="out1" to="out1" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
|
2
|
+
<inputs>
|
3
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
4
|
+
<name>in1</name>
|
5
|
+
<depth>0</depth>
|
6
|
+
<mimeTypes>
|
7
|
+
<string>text/plain</string>
|
8
|
+
</mimeTypes>
|
9
|
+
<handledReferenceSchemes />
|
10
|
+
<translatedElementType>java.lang.String</translatedElementType>
|
11
|
+
<allowsLiteralValues>true</allowsLiteralValues>
|
12
|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
13
|
+
</inputs>
|
14
|
+
<outputs>
|
15
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
16
|
+
<name>out1</name>
|
17
|
+
<depth>0</depth>
|
18
|
+
<mimeTypes />
|
19
|
+
<granularDepth>0</granularDepth>
|
20
|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
21
|
+
</outputs>
|
22
|
+
<classLoaderSharing>workflow</classLoaderSharing>
|
23
|
+
<localDependencies />
|
24
|
+
<artifactDependencies />
|
25
|
+
<script>String out1 = in1;</script>
|
26
|
+
<dependencies />
|
27
|
+
</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>1.4</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="">
|
28
|
+
<maxJobs>1</maxJobs>
|
29
|
+
</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>1.4</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>1.4</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>1.4</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="">
|
30
|
+
<backoffFactor>1.0</backoffFactor>
|
31
|
+
<initialDelay>1000</initialDelay>
|
32
|
+
<maxDelay>5000</maxDelay>
|
33
|
+
<maxRetries>0</maxRetries>
|
34
|
+
</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>1.4</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="in1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Create_10_Strings</name><inputPorts /><outputPorts><port><name>strings</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="strings" to="strings" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
35
|
+
<inputs />
|
36
|
+
<outputs>
|
37
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
38
|
+
<name>strings</name>
|
39
|
+
<depth>1</depth>
|
40
|
+
<mimeTypes />
|
41
|
+
<granularDepth>1</granularDepth>
|
42
|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
43
|
+
</outputs>
|
44
|
+
<classLoaderSharing>workflow</classLoaderSharing>
|
45
|
+
<localDependencies />
|
46
|
+
<artifactDependencies />
|
47
|
+
<script>List strings = new ArrayList();
|
48
|
+
for (int i = 0; i < 10; i++) {
|
49
|
+
strings.add("String" + i);
|
50
|
+
}
|
51
|
+
</script>
|
52
|
+
<dependencies />
|
53
|
+
<localworkerName>org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings</localworkerName>
|
54
|
+
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
55
|
+
<annotationAssertions>
|
56
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
57
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">
|
58
|
+
<text>UserNameHere</text>
|
59
|
+
</annotationBean>
|
60
|
+
<date>2013-05-21 15:33:47.569 UTC</date>
|
61
|
+
<creators />
|
62
|
+
<curationEventList />
|
63
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
64
|
+
</annotationAssertions>
|
65
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="">
|
66
|
+
<maxJobs>1</maxJobs>
|
67
|
+
</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>1.4</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>1.4</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>1.4</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="">
|
68
|
+
<backoffFactor>1.0</backoffFactor>
|
69
|
+
<initialDelay>1000</initialDelay>
|
70
|
+
<maxDelay>5000</maxDelay>
|
71
|
+
<maxRetries>0</maxRetries>
|
72
|
+
</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>1.4</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><processor><name>Create_Lists</name><inputPorts /><outputPorts><port><name>strings1</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>strings2</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>strings3</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>strings4</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="strings2" to="strings2" /><map from="strings3" to="strings3" /><map from="strings4" to="strings4" /><map from="strings1" to="strings1" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
73
|
+
<inputs />
|
74
|
+
<outputs>
|
75
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
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<name>strings1</name>
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<depth>1</depth>
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<mimeTypes />
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<granularDepth>1</granularDepth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<name>strings2</name>
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<depth>1</depth>
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<mimeTypes />
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<granularDepth>1</granularDepth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<name>strings3</name>
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<depth>1</depth>
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<mimeTypes />
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<granularDepth>1</granularDepth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<name>strings4</name>
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<depth>1</depth>
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<mimeTypes />
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<granularDepth>1</granularDepth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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</outputs>
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<script>List strings1 = new ArrayList();
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List strings2 = new ArrayList();
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List strings3 = new ArrayList();
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List strings4 = new ArrayList();
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for (int i = 0; i < 10; i++) {
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strings1.add("String" + i);
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strings3.add("String" + i);
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}
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</script>
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<dependencies />
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<localworkerName>org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings</localworkerName>
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</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain 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.HostInstitution">
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<text>UserNameHere</text>
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</annotationBean>
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<date>2013-05-21 15:37:59.152 UTC</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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<maxJobs>1</maxJobs>
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
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<backoffFactor>1.0</backoffFactor>
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<initialDelay>1000</initialDelay>
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<maxDelay>5000</maxDelay>
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<maxRetries>0</maxRetries>
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<name>in1</name>
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<depth>0</depth>
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<mimeTypes>
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<string>text/plain</string>
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</mimeTypes>
|
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<name>out1</name>
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<depth>0</depth>
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<mimeTypes />
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<granularDepth>0</granularDepth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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</outputs>
|
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<script>String out1 = in1;</script>
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<dependencies />
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</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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<maxJobs>1</maxJobs>
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
|
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<backoffFactor>1.0</backoffFactor>
|
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<initialDelay>1000</initialDelay>
|
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<maxDelay>5000</maxDelay>
|
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<maxRetries>0</maxRetries>
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="in1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Create_Deep_List</name><inputPorts /><outputPorts><port><name>meta_list</name><depth>2</depth><granularDepth>2</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="meta_list" to="meta_list" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
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<inputs />
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<outputs>
|
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<name>meta_list</name>
|
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<depth>2</depth>
|
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<mimeTypes />
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<granularDepth>2</granularDepth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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</outputs>
|
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<script>List strings1 = new ArrayList();
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List strings2 = new ArrayList();
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List strings3 = new ArrayList();
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List strings4 = new ArrayList();
|
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for (int i = 0; i < 10; i++) {
|
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strings1.add("String" + i);
|
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strings3.add("String" + i);
|
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}
|
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List meta_list = new ArrayList();
|
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meta_list.add(strings1);
|
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meta_list.add(strings2);
|
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meta_list.add(strings3);
|
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meta_list.add(strings4);</script>
|
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<dependencies />
|
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<localworkerName>org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings</localworkerName>
|
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</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">
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<text>UserNameHere</text>
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</annotationBean>
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<date>2013-05-21 15:39:51.698 UTC</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></annotations></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
|
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<maxJobs>1</maxJobs>
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
|
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<backoffFactor>1.0</backoffFactor>
|
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<initialDelay>1000</initialDelay>
|
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<maxDelay>5000</maxDelay>
|
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<maxRetries>0</maxRetries>
|
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|
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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><processor><name>Passthrough_3</name><inputPorts><port><name>in1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out1</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>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in1" to="in1" /></inputMap><outputMap><map from="out1" to="out1" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
|
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|
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<inputs>
|
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|
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
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|
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<name>in1</name>
|
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|
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<depth>0</depth>
|
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|
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<mimeTypes>
|
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|
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<string>text/plain</string>
|
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|
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</mimeTypes>
|
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|
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<handledReferenceSchemes />
|
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|
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<translatedElementType>java.lang.String</translatedElementType>
|
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|
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<allowsLiteralValues>true</allowsLiteralValues>
|
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|
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
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|
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</inputs>
|
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|
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<outputs>
|
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|
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
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|
+
<name>out1</name>
|
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|
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<depth>0</depth>
|
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|
+
<mimeTypes />
|
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|
+
<granularDepth>0</granularDepth>
|
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|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
231
|
+
</outputs>
|
232
|
+
<classLoaderSharing>workflow</classLoaderSharing>
|
233
|
+
<localDependencies />
|
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|
+
<artifactDependencies />
|
235
|
+
<script>String out1 = in1;</script>
|
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|
+
<dependencies />
|
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|
+
</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>1.4</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="">
|
238
|
+
<maxJobs>1</maxJobs>
|
239
|
+
</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>1.4</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>1.4</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>1.4</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="">
|
240
|
+
<backoffFactor>1.0</backoffFactor>
|
241
|
+
<initialDelay>1000</initialDelay>
|
242
|
+
<maxDelay>5000</maxDelay>
|
243
|
+
<maxRetries>0</maxRetries>
|
244
|
+
</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>1.4</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="in1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Create_Empty_List</name><inputPorts /><outputPorts><port><name>strings</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="strings" to="strings" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
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|
+
<inputs />
|
246
|
+
<outputs>
|
247
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
248
|
+
<name>strings</name>
|
249
|
+
<depth>1</depth>
|
250
|
+
<mimeTypes />
|
251
|
+
<granularDepth>1</granularDepth>
|
252
|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
253
|
+
</outputs>
|
254
|
+
<classLoaderSharing>workflow</classLoaderSharing>
|
255
|
+
<localDependencies />
|
256
|
+
<artifactDependencies />
|
257
|
+
<script>List strings = new ArrayList();
|
258
|
+
</script>
|
259
|
+
<dependencies />
|
260
|
+
<localworkerName>org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings</localworkerName>
|
261
|
+
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
262
|
+
<annotationAssertions>
|
263
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
264
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">
|
265
|
+
<text>UserNameHere</text>
|
266
|
+
</annotationBean>
|
267
|
+
<date>2013-05-21 15:34:28.784 UTC</date>
|
268
|
+
<creators />
|
269
|
+
<curationEventList />
|
270
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
271
|
+
</annotationAssertions>
|
272
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<inputs />
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<name>strings</name>
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<depth>1</depth>
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<mimeTypes />
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<granularDepth>1</granularDepth>
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<script>List strings = new ArrayList();
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for (int i = 0; i < 10; i++) {
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strings.add("String" + i);
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<dependencies />
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<localworkerName>org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings</localworkerName>
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<text>UserNameHere</text>
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<date>2013-05-21 15:33:47.569 UTC</date>
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<maxDelay>5000</maxDelay>
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<maxRetries>0</maxRetries>
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<inputs />
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<name>strings</name>
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<depth>1</depth>
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<mimeTypes />
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<granularDepth>1</granularDepth>
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</outputs>
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<script>List strings = new ArrayList();
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</script>
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<dependencies />
|
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<localworkerName>org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings</localworkerName>
|
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<text>UserNameHere</text>
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</annotationBean>
|
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<date>2013-05-21 15:34:28.784 UTC</date>
|
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<creators />
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<curationEventList />
|
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|
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|
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|
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<maxJobs>1</maxJobs>
|
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|
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<backoffFactor>1.0</backoffFactor>
|
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<initialDelay>1000</initialDelay>
|
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<maxDelay>5000</maxDelay>
|
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<maxRetries>0</maxRetries>
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="processor"><processor>Passthrough_3</processor><port>in1</port></sink><source type="processor"><processor>Create_Deep_List</processor><port>meta_list</port></source></datalink><datalink><sink type="merge"><processor>Passthrough_2</processor><port>in1</port></sink><source type="processor"><processor>Create_Lists</processor><port>strings1</port></source></datalink><datalink><sink type="merge"><processor>Passthrough_2</processor><port>in1</port></sink><source type="processor"><processor>Create_Lists</processor><port>strings2</port></source></datalink><datalink><sink type="merge"><processor>Passthrough_2</processor><port>in1</port></sink><source type="processor"><processor>Create_Lists</processor><port>strings3</port></source></datalink><datalink><sink type="merge"><processor>Passthrough_2</processor><port>in1</port></sink><source type="processor"><processor>Create_Lists</processor><port>strings4</port></source></datalink><datalink><sink type="merge"><processor>Passthrough_1</processor><port>in1</port></sink><source type="processor"><processor>Create_10_Strings</processor><port>strings</port></source></datalink><datalink><sink type="merge"><processor>Passthrough_1</processor><port>in1</port></sink><source type="processor"><processor>Create_Empty_List</processor><port>strings</port></source></datalink><datalink><sink type="merge"><processor>Passthrough_1</processor><port>in1</port></sink><source type="processor"><processor>Create_10_Strings_2</processor><port>strings</port></source></datalink><datalink><sink type="merge"><processor>Passthrough_1</processor><port>in1</port></sink><source type="processor"><processor>Create_Empty_List_2</processor><port>strings</port></source></datalink><datalink><sink type="dataflow"><port>OUT_1</port></sink><source type="processor"><processor>Passthrough_1</processor><port>out1</port></source></datalink><datalink><sink type="dataflow"><port>OUT_2</port></sink><source type="processor"><processor>Passthrough_2</processor><port>out1</port></source></datalink><datalink><sink type="dataflow"><port>OUT_3</port></sink><source type="processor"><processor>Passthrough_3</processor><port>out1</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
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|
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<date>2013-05-21 15:40:13.823 UTC</date>
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<creators />
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<curationEventList />
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
|