taverna-t2flow 0.2.0 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (26) hide show
  1. data/CHANGES.rdoc +16 -0
  2. data/README.rdoc +30 -21
  3. data/Rakefile +54 -0
  4. data/lib/t2flow/model.rb +7 -0
  5. data/lib/t2flow/parser.rb +7 -2
  6. data/taverna-t2flow.gemspec +76 -0
  7. data/test/fixtures/1000.t2flow +244 -0
  8. data/test/fixtures/1001.t2flow +321 -0
  9. data/test/fixtures/1002.t2flow +474 -0
  10. data/test/fixtures/1003.t2flow +292 -0
  11. data/test/fixtures/1004.t2flow +73 -0
  12. data/test/fixtures/996.t2flow +193 -0
  13. data/test/fixtures/997.t2flow +359 -0
  14. data/test/fixtures/998.t2flow +324 -0
  15. data/test/fixtures/999.t2flow +604 -0
  16. data/test/fixtures/basic.t2flow +94 -0
  17. data/test/fixtures/coordinated.t2flow +63 -0
  18. data/test/fixtures/linked.t2flow +88 -0
  19. data/test/fixtures/nested.t2flow +270 -0
  20. data/test/fixtures/processors.t2flow +174 -0
  21. data/test/run_tests.rb +7 -0
  22. data/test/test_bogus_workflows.rb +80 -0
  23. data/test/test_helper.rb +50 -0
  24. data/test/test_starter_pack_workflows.rb +132 -0
  25. metadata +121 -69
  26. data/ChangeLog.rdoc +0 -7
data/test/fixtures/1002.t2flow ADDED
@@ -0,0 +1,474 @@
1
+ <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0"><dataflow id="f0fac9a7-7943-4191-a0d3-7e8e09044e43" role="top"><name>GBSeq_test</name><inputPorts /><outputPorts><port><name>nuc_fasta</name><annotations /></port><port><name>nuc_xml</name><annotations /></port><port><name>nuc_insd</name><annotations /></port><port><name>nuc_tiny</name><annotations /></port><port><name>prot_fasta</name><annotations /></port><port><name>protein_xml</name><annotations /></port><port><name>prot_insd</name><annotations /></port><port><name>prot_tiny</name><annotations /></port></outputPorts><processors><processor><name>nuc_id</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>1.0</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>NM_000059</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>1.0</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>1.0</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>1.0</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>1.0</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>1000</initialDelay>
8
+ <maxDelay>5000</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>1.0</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>protein_id</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>1.0</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>NP_000050</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>1.0</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>1.0</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>1.0</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>1.0</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>1000</initialDelay>
17
+ <maxDelay>5000</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>1.0</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>Get_Nucleotide_INSDSeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
20
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker</localworkerName>
21
+ <script>if ((id == void) || (id == null) || id.equals("")) {
22
+ throw new RunTimeException("port id must have a non-empty value");
23
+ }
24
+
25
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&amp;db=nucleotide&amp;retmode=xml&amp;id=" + id);
26
+
27
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
28
+ StringWriter writer = new StringWriter();
29
+
30
+ char[] buffer = new char[1024];
31
+ while (true) {
32
+ int r = reader.read(buffer);
33
+ if (r &lt;= 0) {
34
+ break;
35
+ }
36
+ writer.write(buffer, 0, r);
37
+ }
38
+ outputText = writer.toString();
39
+ </script>
40
+ <dependencies />
41
+ <classLoaderSharing>workflow</classLoaderSharing>
42
+ <localDependencies />
43
+ <artifactDependencies />
44
+ <inputs>
45
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
46
+ <handledReferenceSchemes />
47
+ <translatedElementType>java.lang.String</translatedElementType>
48
+ <allowsLiteralValues>true</allowsLiteralValues>
49
+ <name>id</name>
50
+ <depth>0</depth>
51
+ <mimeTypes>
52
+ <string>'text/plain'</string>
53
+ </mimeTypes>
54
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
55
+ </inputs>
56
+ <outputs>
57
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
58
+ <granularDepth>0</granularDepth>
59
+ <name>outputText</name>
60
+ <depth>0</depth>
61
+ <mimeTypes>
62
+ <string>'text/plain'</string>
63
+ </mimeTypes>
64
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
65
+ </outputs>
66
+ </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>1.0</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="">
67
+ <maxJobs>1</maxJobs>
68
+ </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>1.0</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>1.0</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>1.0</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="">
69
+ <backoffFactor>1.0</backoffFactor>
70
+ <initialDelay>1000</initialDelay>
71
+ <maxDelay>5000</maxDelay>
72
+ <maxRetries>0</maxRetries>
73
+ </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>1.0</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_FASTA</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
74
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker</localworkerName>
75
+ <script>if ((id == void) || (id == null) || id.equals("")) {
76
+ throw new RunTimeException("port id must have a non-empty value");
77
+ }
78
+
79
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=nucleotide&amp;retmode=text&amp;id=" + id);
80
+
81
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
82
+ StringWriter writer = new StringWriter();
83
+
84
+ char[] buffer = new char[1024];
85
+ while (true) {
86
+ int r = reader.read(buffer);
87
+ if (r &lt;= 0) {
88
+ break;
89
+ }
90
+ writer.write(buffer, 0, r);
91
+ }
92
+ outputText = writer.toString();
93
+ </script>
94
+ <dependencies />
95
+ <classLoaderSharing>workflow</classLoaderSharing>
96
+ <localDependencies />
97
+ <artifactDependencies />
98
+ <inputs>
99
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
100
+ <handledReferenceSchemes />
101
+ <translatedElementType>java.lang.String</translatedElementType>
102
+ <allowsLiteralValues>true</allowsLiteralValues>
103
+ <name>id</name>
104
+ <depth>0</depth>
105
+ <mimeTypes>
106
+ <string>'text/plain'</string>
107
+ </mimeTypes>
108
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
109
+ </inputs>
110
+ <outputs>
111
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
112
+ <granularDepth>0</granularDepth>
113
+ <name>outputText</name>
114
+ <depth>0</depth>
115
+ <mimeTypes>
116
+ <string>'text/plain'</string>
117
+ </mimeTypes>
118
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
119
+ </outputs>
120
+ </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>1.0</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="">
121
+ <maxJobs>1</maxJobs>
122
+ </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>1.0</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>1.0</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>1.0</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="">
123
+ <backoffFactor>1.0</backoffFactor>
124
+ <initialDelay>1000</initialDelay>
125
+ <maxDelay>5000</maxDelay>
126
+ <maxRetries>0</maxRetries>
127
+ </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>1.0</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_GBSeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
128
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker</localworkerName>
129
+ <script>if ((id == void) || (id == null) || id.equals("")) {
130
+ throw new RunTimeException("port id must have a non-empty value");
131
+ }
132
+
133
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&amp;db=nucleotide&amp;retmode=xml&amp;id=" + id);
134
+
135
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
136
+ StringWriter writer = new StringWriter();
137
+
138
+ char[] buffer = new char[1024];
139
+ while (true) {
140
+ int r = reader.read(buffer);
141
+ if (r &lt;= 0) {
142
+ break;
143
+ }
144
+ writer.write(buffer, 0, r);
145
+ }
146
+ outputText = writer.toString();
147
+ </script>
148
+ <dependencies />
149
+ <classLoaderSharing>workflow</classLoaderSharing>
150
+ <localDependencies />
151
+ <artifactDependencies />
152
+ <inputs>
153
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
154
+ <handledReferenceSchemes />
155
+ <translatedElementType>java.lang.String</translatedElementType>
156
+ <allowsLiteralValues>true</allowsLiteralValues>
157
+ <name>id</name>
158
+ <depth>0</depth>
159
+ <mimeTypes>
160
+ <string>'text/plain'</string>
161
+ </mimeTypes>
162
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
163
+ </inputs>
164
+ <outputs>
165
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
166
+ <granularDepth>0</granularDepth>
167
+ <name>outputText</name>
168
+ <depth>0</depth>
169
+ <mimeTypes>
170
+ <string>'text/plain'</string>
171
+ </mimeTypes>
172
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
173
+ </outputs>
174
+ </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>1.0</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="">
175
+ <maxJobs>1</maxJobs>
176
+ </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>1.0</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>1.0</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>1.0</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="">
177
+ <backoffFactor>1.0</backoffFactor>
178
+ <initialDelay>1000</initialDelay>
179
+ <maxDelay>5000</maxDelay>
180
+ <maxRetries>0</maxRetries>
181
+ </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>1.0</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_TinySeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
182
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker</localworkerName>
183
+ <script>if ((id == void) || (id == null) || id.equals("")) {
184
+ throw new RunTimeException("port id must have a non-empty value");
185
+ }
186
+
187
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=nucleotide&amp;retmode=xml&amp;id=" + id);
188
+
189
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
190
+ StringWriter writer = new StringWriter();
191
+
192
+ char[] buffer = new char[1024];
193
+ while (true) {
194
+ int r = reader.read(buffer);
195
+ if (r &lt;= 0) {
196
+ break;
197
+ }
198
+ writer.write(buffer, 0, r);
199
+ }
200
+ outputText = writer.toString();
201
+ </script>
202
+ <dependencies />
203
+ <classLoaderSharing>workflow</classLoaderSharing>
204
+ <localDependencies />
205
+ <artifactDependencies />
206
+ <inputs>
207
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
208
+ <handledReferenceSchemes />
209
+ <translatedElementType>java.lang.String</translatedElementType>
210
+ <allowsLiteralValues>true</allowsLiteralValues>
211
+ <name>id</name>
212
+ <depth>0</depth>
213
+ <mimeTypes>
214
+ <string>'text/plain'</string>
215
+ </mimeTypes>
216
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
217
+ </inputs>
218
+ <outputs>
219
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
220
+ <granularDepth>0</granularDepth>
221
+ <name>outputText</name>
222
+ <depth>0</depth>
223
+ <mimeTypes>
224
+ <string>'text/plain'</string>
225
+ </mimeTypes>
226
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
227
+ </outputs>
228
+ </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>1.0</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="">
229
+ <maxJobs>1</maxJobs>
230
+ </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>1.0</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>1.0</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>1.0</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="">
231
+ <backoffFactor>1.0</backoffFactor>
232
+ <initialDelay>1000</initialDelay>
233
+ <maxDelay>5000</maxDelay>
234
+ <maxRetries>0</maxRetries>
235
+ </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>1.0</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Protein_FASTA</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
236
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker</localworkerName>
237
+ <script>if ((id == void) || (id == null) || id.equals("")) {
238
+ throw new RunTimeException("port id must have a non-empty value");
239
+ }
240
+
241
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=protein&amp;retmode=text&amp;id=" + id);
242
+
243
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
244
+ StringWriter writer = new StringWriter();
245
+
246
+ char[] buffer = new char[1024];
247
+ while (true) {
248
+ int r = reader.read(buffer);
249
+ if (r &lt;= 0) {
250
+ break;
251
+ }
252
+ writer.write(buffer, 0, r);
253
+ }
254
+ outputText = writer.toString();
255
+ </script>
256
+ <dependencies />
257
+ <classLoaderSharing>workflow</classLoaderSharing>
258
+ <localDependencies />
259
+ <artifactDependencies />
260
+ <inputs>
261
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
262
+ <handledReferenceSchemes />
263
+ <translatedElementType>java.lang.String</translatedElementType>
264
+ <allowsLiteralValues>true</allowsLiteralValues>
265
+ <name>id</name>
266
+ <depth>0</depth>
267
+ <mimeTypes>
268
+ <string>'text/plain'</string>
269
+ </mimeTypes>
270
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
271
+ </inputs>
272
+ <outputs>
273
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
274
+ <granularDepth>0</granularDepth>
275
+ <name>outputText</name>
276
+ <depth>0</depth>
277
+ <mimeTypes>
278
+ <string>'text/plain'</string>
279
+ </mimeTypes>
280
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
281
+ </outputs>
282
+ </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>1.0</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="">
283
+ <maxJobs>1</maxJobs>
284
+ </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>1.0</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>1.0</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>1.0</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="">
285
+ <backoffFactor>1.0</backoffFactor>
286
+ <initialDelay>1000</initialDelay>
287
+ <maxDelay>5000</maxDelay>
288
+ <maxRetries>0</maxRetries>
289
+ </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>1.0</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Protein_INSDSeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
290
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker</localworkerName>
291
+ <script>if ((id == void) || (id == null) || id.equals("")) {
292
+ throw new RunTimeException("port id must have a non-empty value");
293
+ }
294
+
295
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&amp;db=protein&amp;retmode=xml&amp;id=" + id);
296
+
297
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
298
+ StringWriter writer = new StringWriter();
299
+
300
+ char[] buffer = new char[1024];
301
+ while (true) {
302
+ int r = reader.read(buffer);
303
+ if (r &lt;= 0) {
304
+ break;
305
+ }
306
+ writer.write(buffer, 0, r);
307
+ }
308
+ outputText = writer.toString();
309
+ </script>
310
+ <dependencies />
311
+ <classLoaderSharing>workflow</classLoaderSharing>
312
+ <localDependencies />
313
+ <artifactDependencies />
314
+ <inputs>
315
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
316
+ <handledReferenceSchemes />
317
+ <translatedElementType>java.lang.String</translatedElementType>
318
+ <allowsLiteralValues>true</allowsLiteralValues>
319
+ <name>id</name>
320
+ <depth>0</depth>
321
+ <mimeTypes>
322
+ <string>'text/plain'</string>
323
+ </mimeTypes>
324
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
325
+ </inputs>
326
+ <outputs>
327
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
328
+ <granularDepth>0</granularDepth>
329
+ <name>outputText</name>
330
+ <depth>0</depth>
331
+ <mimeTypes>
332
+ <string>'text/plain'</string>
333
+ </mimeTypes>
334
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
335
+ </outputs>
336
+ </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>1.0</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="">
337
+ <maxJobs>1</maxJobs>
338
+ </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>1.0</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>1.0</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>1.0</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="">
339
+ <backoffFactor>1.0</backoffFactor>
340
+ <initialDelay>1000</initialDelay>
341
+ <maxDelay>5000</maxDelay>
342
+ <maxRetries>0</maxRetries>
343
+ </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>1.0</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Protein_TinySeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
344
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker</localworkerName>
345
+ <script>if ((id == void) || (id == null) || id.equals("")) {
346
+ throw new RunTimeException("port id must have a non-empty value");
347
+ }
348
+
349
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=protein&amp;retmode=xml&amp;id=" + id);
350
+
351
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
352
+ StringWriter writer = new StringWriter();
353
+
354
+ char[] buffer = new char[1024];
355
+ while (true) {
356
+ int r = reader.read(buffer);
357
+ if (r &lt;= 0) {
358
+ break;
359
+ }
360
+ writer.write(buffer, 0, r);
361
+ }
362
+ outputText = writer.toString();
363
+ </script>
364
+ <dependencies />
365
+ <classLoaderSharing>workflow</classLoaderSharing>
366
+ <localDependencies />
367
+ <artifactDependencies />
368
+ <inputs>
369
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
370
+ <handledReferenceSchemes />
371
+ <translatedElementType>java.lang.String</translatedElementType>
372
+ <allowsLiteralValues>true</allowsLiteralValues>
373
+ <name>id</name>
374
+ <depth>0</depth>
375
+ <mimeTypes>
376
+ <string>'text/plain'</string>
377
+ </mimeTypes>
378
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
379
+ </inputs>
380
+ <outputs>
381
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
382
+ <granularDepth>0</granularDepth>
383
+ <name>outputText</name>
384
+ <depth>0</depth>
385
+ <mimeTypes>
386
+ <string>'text/plain'</string>
387
+ </mimeTypes>
388
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
389
+ </outputs>
390
+ </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>1.0</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="">
391
+ <maxJobs>1</maxJobs>
392
+ </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>1.0</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>1.0</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>1.0</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="">
393
+ <backoffFactor>1.0</backoffFactor>
394
+ <initialDelay>1000</initialDelay>
395
+ <maxDelay>5000</maxDelay>
396
+ <maxRetries>0</maxRetries>
397
+ </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>1.0</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Protein_GBSeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
398
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker</localworkerName>
399
+ <script>if ((id == void) || (id == null) || id.equals("")) {
400
+ throw new RunTimeException("port id must have a non-empty value");
401
+ }
402
+
403
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&amp;db=protein&amp;retmode=xml&amp;id=" + id);
404
+
405
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
406
+ StringWriter writer = new StringWriter();
407
+
408
+ char[] buffer = new char[1024];
409
+ while (true) {
410
+ int r = reader.read(buffer);
411
+ if (r &lt;= 0) {
412
+ break;
413
+ }
414
+ writer.write(buffer, 0, r);
415
+ }
416
+ outputText = writer.toString();
417
+ </script>
418
+ <dependencies />
419
+ <classLoaderSharing>workflow</classLoaderSharing>
420
+ <localDependencies />
421
+ <artifactDependencies />
422
+ <inputs>
423
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
424
+ <handledReferenceSchemes />
425
+ <translatedElementType>java.lang.String</translatedElementType>
426
+ <allowsLiteralValues>true</allowsLiteralValues>
427
+ <name>id</name>
428
+ <depth>0</depth>
429
+ <mimeTypes>
430
+ <string>'text/plain'</string>
431
+ </mimeTypes>
432
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
433
+ </inputs>
434
+ <outputs>
435
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
436
+ <granularDepth>0</granularDepth>
437
+ <name>outputText</name>
438
+ <depth>0</depth>
439
+ <mimeTypes>
440
+ <string>'text/plain'</string>
441
+ </mimeTypes>
442
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
443
+ </outputs>
444
+ </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>1.0</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="">
445
+ <maxJobs>1</maxJobs>
446
+ </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>1.0</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>1.0</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>1.0</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="">
447
+ <backoffFactor>1.0</backoffFactor>
448
+ <initialDelay>1000</initialDelay>
449
+ <maxDelay>5000</maxDelay>
450
+ <maxRetries>0</maxRetries>
451
+ </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>1.0</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Get_Nucleotide_INSDSeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Nucleotide_FASTA</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Nucleotide_GBSeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Nucleotide_TinySeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_FASTA</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_INSDSeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_TinySeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_GBSeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>nuc_fasta</port></sink><source type="processor"><processor>Get_Nucleotide_FASTA</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_xml</port></sink><source type="processor"><processor>Get_Nucleotide_GBSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_insd</port></sink><source type="processor"><processor>Get_Nucleotide_INSDSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_tiny</port></sink><source type="processor"><processor>Get_Nucleotide_TinySeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_fasta</port></sink><source type="processor"><processor>Get_Protein_FASTA</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>protein_xml</port></sink><source type="processor"><processor>Get_Protein_GBSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_insd</port></sink><source type="processor"><processor>Get_Protein_INSDSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_tiny</port></sink><source type="processor"><processor>Get_Protein_TinySeq_XML</processor><port>outputText</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
452
+ <annotationAssertions>
453
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
454
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
455
+ <text>GBSeq test</text>
456
+ </annotationBean>
457
+ <date>2009-12-15 20:30:12.959 GMT</date>
458
+ <creators />
459
+ <curationEventList />
460
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
461
+ </annotationAssertions>
462
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
463
+ <annotationAssertions>
464
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
465
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
466
+ <text>This workflow retrieves nucleotide and protein sequences with the literature and references associated
467
+ to them given a protein and a nucleotide id.</text>
468
+ </annotationBean>
469
+ <date>2009-12-15 20:30:23.505 GMT</date>
470
+ <creators />
471
+ <curationEventList />
472
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
473
+ </annotationAssertions>
474
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>