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Posted to commits@taverna.apache.org by st...@apache.org on 2015/03/17 10:39:24 UTC
[1/9] incubator-taverna-language git commit: Strip out actual content
from COMBINE test archives
Repository: incubator-taverna-language
Updated Branches:
refs/heads/master cb2e77f33 -> 3d74eb6e2
Strip out actual content from COMBINE test archives
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/11aa3c0b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/11aa3c0b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/11aa3c0b
Branch: refs/heads/master
Commit: 11aa3c0b3b96143b261763fe0163132bdc114263
Parents: cb2e77f
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:03:32 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:03:32 2015 +0000
----------------------------------------------------------------------
.../manifest/combine/TestCombineManifest.java | 8 ++++----
.../test/resources/combine/Boris-skeleton.omex | Bin 0 -> 1449 bytes
.../src/test/resources/combine/Boris.omex | Bin 355256 -> 0 bytes
.../combine/DirectoryMadness-skeleton.omex | Bin 0 -> 2189 bytes
.../test/resources/combine/DirectoryMadness.omex | Bin 355078 -> 0 bytes
.../combine/DirectoryMadnessZipped-skeleton.omex | Bin 0 -> 2188 bytes
.../resources/combine/DirectoryMadnessZipped.omex | Bin 353871 -> 0 bytes
.../combine/aslanidi_purkinje_model_2009.zip | Bin 896049 -> 0 bytes
.../combine/aslanidi_purkinje_model_skeleton.zip | Bin 0 -> 6620 bytes
9 files changed, 4 insertions(+), 4 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
index 5286d67..7fc54ed 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
@@ -41,7 +41,7 @@ public class TestCombineManifest {
public void convertAslanidi() throws Exception {
Path file = Files.createTempFile("aslanidi", ".zip");
try (InputStream src = getClass().getResourceAsStream(
- "/combine/aslanidi_purkinje_model_2009.zip")) {
+ "/combine/aslanidi_purkinje_model_skeleton.zip")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
System.out.println(file);
@@ -75,7 +75,7 @@ public class TestCombineManifest {
public void convertBoris() throws Exception {
Path file = Files.createTempFile("Boris", ".omex");
try (InputStream src = getClass().getResourceAsStream(
- "/combine/Boris.omex")) {
+ "/combine/Boris-skeleton.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
//System.out.println(file);
@@ -103,7 +103,7 @@ public class TestCombineManifest {
public void convertDirectoryMadness() throws Exception {
Path file = Files.createTempFile("DirectoryMadness", ".omex");
try (InputStream src = getClass().getResourceAsStream(
- "/combine/DirectoryMadness.omex")) {
+ "/combine/DirectoryMadness-skeleton.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
//System.out.println(file);
@@ -143,7 +143,7 @@ public class TestCombineManifest {
public void convertDirectoryMadnessZipped() throws Exception {
Path file = Files.createTempFile("DirectoryMadnessZipped", ".omex");
try (InputStream src = getClass().getResourceAsStream(
- "/combine/DirectoryMadnessZipped.omex")) {
+ "/combine/DirectoryMadnessZipped-skeleton.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
//System.out.println(file);
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/resources/combine/Boris-skeleton.omex
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/combine/Boris-skeleton.omex b/taverna-robundle/src/test/resources/combine/Boris-skeleton.omex
new file mode 100644
index 0000000..2c31167
Binary files /dev/null and b/taverna-robundle/src/test/resources/combine/Boris-skeleton.omex differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/resources/combine/Boris.omex
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/combine/Boris.omex b/taverna-robundle/src/test/resources/combine/Boris.omex
deleted file mode 100644
index a4d5cf4..0000000
Binary files a/taverna-robundle/src/test/resources/combine/Boris.omex and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/resources/combine/DirectoryMadness-skeleton.omex
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/combine/DirectoryMadness-skeleton.omex b/taverna-robundle/src/test/resources/combine/DirectoryMadness-skeleton.omex
new file mode 100644
index 0000000..955ad13
Binary files /dev/null and b/taverna-robundle/src/test/resources/combine/DirectoryMadness-skeleton.omex differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/resources/combine/DirectoryMadness.omex
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/combine/DirectoryMadness.omex b/taverna-robundle/src/test/resources/combine/DirectoryMadness.omex
deleted file mode 100644
index 4721646..0000000
Binary files a/taverna-robundle/src/test/resources/combine/DirectoryMadness.omex and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/resources/combine/DirectoryMadnessZipped-skeleton.omex
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/combine/DirectoryMadnessZipped-skeleton.omex b/taverna-robundle/src/test/resources/combine/DirectoryMadnessZipped-skeleton.omex
new file mode 100644
index 0000000..9abe68e
Binary files /dev/null and b/taverna-robundle/src/test/resources/combine/DirectoryMadnessZipped-skeleton.omex differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/resources/combine/DirectoryMadnessZipped.omex
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/combine/DirectoryMadnessZipped.omex b/taverna-robundle/src/test/resources/combine/DirectoryMadnessZipped.omex
deleted file mode 100644
index 3fff30c..0000000
Binary files a/taverna-robundle/src/test/resources/combine/DirectoryMadnessZipped.omex and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/resources/combine/aslanidi_purkinje_model_2009.zip
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/combine/aslanidi_purkinje_model_2009.zip b/taverna-robundle/src/test/resources/combine/aslanidi_purkinje_model_2009.zip
deleted file mode 100644
index 0ccb776..0000000
Binary files a/taverna-robundle/src/test/resources/combine/aslanidi_purkinje_model_2009.zip and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/11aa3c0b/taverna-robundle/src/test/resources/combine/aslanidi_purkinje_model_skeleton.zip
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/combine/aslanidi_purkinje_model_skeleton.zip b/taverna-robundle/src/test/resources/combine/aslanidi_purkinje_model_skeleton.zip
new file mode 100644
index 0000000..68b5bfa
Binary files /dev/null and b/taverna-robundle/src/test/resources/combine/aslanidi_purkinje_model_skeleton.zip differ
[5/9] incubator-taverna-language git commit: Apache headers
Posted by st...@apache.org.
Apache headers
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/fc071a6d
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/fc071a6d
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/fc071a6d
Branch: refs/heads/master
Commit: fc071a6da17906d33559f283525600723d233680
Parents: bbad186
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:09:40 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:09:40 2015 +0000
----------------------------------------------------------------------
.../T3-1226-annotations-with-quotes.t2flow | 32 ++++++++---------
.../src/test/resources/helloanyone.t2flow | 36 +++++++++-----------
.../src/test/resources/helloworld.t2flow | 36 +++++++++-----------
3 files changed, 50 insertions(+), 54 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/fc071a6d/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow b/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow
index 0bf8dd0..3f9aa3e 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow
@@ -20,10 +20,10 @@
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-workbench-core-2.5.0-20140804T1456"><dataflow id="73a04132-5dc0-4e24-8a30-6ef91c773ad1" role="top"><name>T3_1226_test_with__s</name><inputPorts><port><name>a</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
- <text>quote at the end"</text>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>"quote at the start</text>
</annotationBean>
- <date>2014-12-08 12:28:50.238 UTC</date>
+ <date>2014-12-08 12:28:56.410 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
@@ -31,10 +31,10 @@
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>"quote at the start</text>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>quote at the end"</text>
</annotationBean>
- <date>2014-12-08 12:28:56.410 UTC</date>
+ <date>2014-12-08 12:28:50.238 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
@@ -61,18 +61,18 @@
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This comment contains """triple quotes""" inside.</text>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>bb55dae2-8d6e-4971-9694-9e4beaccca46</identification>
</annotationBean>
- <date>2014-12-08 12:29:12.250 UTC</date>
+ <date>2014-12-08 12:29:50.55 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
@@ -83,15 +83,15 @@
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>bb55dae2-8d6e-4971-9694-9e4beaccca46</identification>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>This comment contains """triple quotes""" inside.</text>
</annotationBean>
- <date>2014-12-08 12:29:50.55 UTC</date>
+ <date>2014-12-08 12:29:12.250 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/fc071a6d/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow b/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
index 3b625f1..2e100b1 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
@@ -1,22 +1,20 @@
-<?xml version="1.0"?>
-<!--
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- -->
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="01348671-5aaa-4cc2-84cc-477329b70b0d" role="top"><name>Hello_Anyone</name><inputPorts><port><name>name</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/fc071a6d/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow b/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
index 2e10ed9..2991433 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
@@ -1,22 +1,20 @@
-<?xml version="1.0"?>
-<!--
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- -->
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="8781d5f4-d0ba-48a8-a1d1-14281bd8a917" role="top"><name>Hello_World</name><inputPorts /><outputPorts><port><name>greeting</name><annotations /></port></outputPorts><processors><processor><name>hello</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
<value>Hello, World!</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
[8/9] incubator-taverna-language git commit: Apache license headers
.. on our files
Posted by st...@apache.org.
Apache license headers .. on our files
enm-v21 is not fully ours, so has to go
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/2f46d8d8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/2f46d8d8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/2f46d8d8
Branch: refs/heads/master
Commit: 2f46d8d805782bc40b06f9913bcfd44acab9ef4b
Parents: fc071a6
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:38:32 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:38:32 2015 +0000
----------------------------------------------------------------------
.../test/resources/allTypes.links.sparql.json | 93 +-
.../src/test/resources/enm-v21.t2flow | 30875 -----------------
.../src/test/resources/helloworld.wfdesc.ttl | 16 +
.../src/test/resources/localdependency.t2flow | 21 +-
.../src/test/resources/nested.t2flow | 21 +-
.../resources/rdf-in-example-annotation.t2flow | 21 +-
.../valid_component_imagemagickconvert.t2flow | 19 +
7 files changed, 142 insertions(+), 30924 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2f46d8d8/taverna-scufl2-wfdesc/src/test/resources/allTypes.links.sparql.json
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/allTypes.links.sparql.json b/taverna-scufl2-wfdesc/src/test/resources/allTypes.links.sparql.json
index 578cb8a..f018b9b 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/allTypes.links.sparql.json
+++ b/taverna-scufl2-wfdesc/src/test/resources/allTypes.links.sparql.json
@@ -1,72 +1,73 @@
{
+ "__license__": "Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under the Apache License, Version 2.0 (the 'License'); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an 'AS IS' BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.",
"head": {
"vars": [ "wf", "fromProc", "toProc", "fromProcLabel", "toProcLabel" ]
- },
+ },
"results": {
"bindings": [
{
- "toProcLabel": { "type": "literal", "value": "theWsdl" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theWsdl\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theBeanshell\/" },
+ "toProcLabel": { "type": "literal", "value": "theWsdl" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theWsdl\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theBeanshell\/" },
"fromProcLabel": { "type": "literal", "value": "theBeanshell" }
- },
+ },
{
- "toProcLabel": { "type": "literal", "value": "theXPath" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theXPath\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theNested\/" },
+ "toProcLabel": { "type": "literal", "value": "theXPath" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theXPath\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theNested\/" },
"fromProcLabel": { "type": "literal", "value": "theNested" }
- },
+ },
{
- "toProcLabel": { "type": "literal", "value": "theSpreadsheet" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theSpreadsheet\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theREST\/" },
+ "toProcLabel": { "type": "literal", "value": "theSpreadsheet" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theSpreadsheet\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theREST\/" },
"fromProcLabel": { "type": "literal", "value": "theREST" }
- },
+ },
{
- "toProcLabel": { "type": "literal", "value": "theNested" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theNested\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theSpreadsheet\/" },
+ "toProcLabel": { "type": "literal", "value": "theNested" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theNested\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theSpreadsheet\/" },
"fromProcLabel": { "type": "literal", "value": "theSpreadsheet" }
- },
+ },
{
- "toProcLabel": { "type": "literal", "value": "theREST" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theREST\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theText\/" },
+ "toProcLabel": { "type": "literal", "value": "theREST" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theREST\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theText\/" },
"fromProcLabel": { "type": "literal", "value": "theText" }
- },
+ },
{
- "toProcLabel": { "type": "literal", "value": "theRscript" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theRscript\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theTool\/" },
+ "toProcLabel": { "type": "literal", "value": "theRscript" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theRscript\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theTool\/" },
"fromProcLabel": { "type": "literal", "value": "theTool" }
- },
+ },
{
- "toProcLabel": { "type": "literal", "value": "theToolRepository" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theToolRepository\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theTool\/" },
+ "toProcLabel": { "type": "literal", "value": "theToolRepository" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theToolRepository\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theTool\/" },
"fromProcLabel": { "type": "literal", "value": "theTool" }
- },
+ },
{
- "toProcLabel": { "type": "literal", "value": "theToolRepository" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theToolRepository\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theWsdl\/" },
+ "toProcLabel": { "type": "literal", "value": "theToolRepository" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theToolRepository\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theWsdl\/" },
"fromProcLabel": { "type": "literal", "value": "theWsdl" }
- },
+ },
{
- "toProcLabel": { "type": "literal", "value": "theWsdl" },
- "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theWsdl\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theXPath\/" },
+ "toProcLabel": { "type": "literal", "value": "theWsdl" },
+ "toProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theWsdl\/" },
+ "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
+ "fromProc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theXPath\/" },
"fromProcLabel": { "type": "literal", "value": "theXPath" }
}
]
}
-}
\ No newline at end of file
+}
[4/9] incubator-taverna-language git commit: LICENSE file
Posted by st...@apache.org.
LICENSE file
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/bbad186c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/bbad186c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/bbad186c
Branch: refs/heads/master
Commit: bbad186c78db0727f7be084d0fac7fdb172ddd94
Parents: 42eb15a
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:07:09 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:07:09 2015 +0000
----------------------------------------------------------------------
.../src/test/resources/document.odt | Bin 10372 -> 13938 bytes
.../src/test/resources/helloworld.wfbundle | Bin 6637 -> 10155 bytes
.../src/test/resources/workflowrun.bundle.zip | Bin 4126 -> 7740 bytes
3 files changed, 0 insertions(+), 0 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bbad186c/taverna-robundle/src/test/resources/document.odt
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/document.odt b/taverna-robundle/src/test/resources/document.odt
index 6dc7126..f1be74a 100644
Binary files a/taverna-robundle/src/test/resources/document.odt and b/taverna-robundle/src/test/resources/document.odt differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bbad186c/taverna-robundle/src/test/resources/helloworld.wfbundle
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/helloworld.wfbundle b/taverna-robundle/src/test/resources/helloworld.wfbundle
index ed4cd76..0b981aa 100644
Binary files a/taverna-robundle/src/test/resources/helloworld.wfbundle and b/taverna-robundle/src/test/resources/helloworld.wfbundle differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bbad186c/taverna-robundle/src/test/resources/workflowrun.bundle.zip
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/workflowrun.bundle.zip b/taverna-robundle/src/test/resources/workflowrun.bundle.zip
index 00b4aec..1c4becb 100644
Binary files a/taverna-robundle/src/test/resources/workflowrun.bundle.zip and b/taverna-robundle/src/test/resources/workflowrun.bundle.zip differ
[6/9] incubator-taverna-language git commit: Apache license headers
.. on our files
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2f46d8d8/taverna-scufl2-wfdesc/src/test/resources/helloworld.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/helloworld.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/helloworld.wfdesc.ttl
index ac25e5b..e8297b1 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/helloworld.wfdesc.ttl
+++ b/taverna-scufl2-wfdesc/src/test/resources/helloworld.wfdesc.ttl
@@ -1,3 +1,19 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
@base <http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/workflow/Hello_World/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2f46d8d8/taverna-scufl2-wfdesc/src/test/resources/localdependency.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/localdependency.t2flow b/taverna-scufl2-wfdesc/src/test/resources/localdependency.t2flow
index 2e646df..289d22e 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/localdependency.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/localdependency.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="024011b4-bc92-4836-8043-6e787cfc72b7" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Beanshell</name><inputPorts /><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 /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<inputs />
<outputs />
@@ -26,4 +45,4 @@
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2f46d8d8/taverna-scufl2-wfdesc/src/test/resources/nested.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/nested.t2flow b/taverna-scufl2-wfdesc/src/test/resources/nested.t2flow
index b80054e..5d4601b 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/nested.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/nested.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="91a0588a-1058-47ba-b0e0-4bbb5d004c38" role="top"><name>Workflow6</name><inputPorts /><outputPorts><port><name>listC</name><annotations /></port></outputPorts><processors><processor><name>Create_Lots_Of_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="">
<inputs />
<outputs>
@@ -225,4 +244,4 @@ concatenated = sb.toString();
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2f46d8d8/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.t2flow b/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.t2flow
index 7d782d5..e43c493 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-core-2.5.0"><dataflow id="b9ca25c7-f594-47c1-af62-af9d380002c8" role="top"><name>Workflow4</name><inputPorts><port><name>example</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
@@ -24,4 +43,4 @@
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2f46d8d8/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.t2flow b/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.t2flow
index 89489cf..3c517e9 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="8d2f9ef0-09ca-4103-b4fd-0ee0a40d8263" role="top"><name>Imagemagick_convert_</name><inputPorts><port><name>from_uri</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
[2/9] incubator-taverna-language git commit: Removed motifAnalysis as
it was licensed as CC-NC
Posted by st...@apache.org.
Removed motifAnalysis as it was licensed as CC-NC
CreativeCommons non-commercial
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/a61518d0
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/a61518d0
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/a61518d0
Branch: refs/heads/master
Commit: a61518d050c690d57ad11e26a3fb8e926b6c509b
Parents: 11aa3c0
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:04:41 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:04:41 2015 +0000
----------------------------------------------------------------------
.../src/test/resources/motifAnalysis.zip | Bin 6936503 -> 0 bytes
1 file changed, 0 insertions(+), 0 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a61518d0/taverna-robundle/src/test/resources/motifAnalysis.zip
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/resources/motifAnalysis.zip b/taverna-robundle/src/test/resources/motifAnalysis.zip
deleted file mode 100644
index 66b59f2..0000000
Binary files a/taverna-robundle/src/test/resources/motifAnalysis.zip and /dev/null differ
[7/9] incubator-taverna-language git commit: Apache license headers
.. on our files
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2f46d8d8/taverna-scufl2-wfdesc/src/test/resources/enm-v21.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/enm-v21.t2flow b/taverna-scufl2-wfdesc/src/test/resources/enm-v21.t2flow
deleted file mode 100644
index eb64c77..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/enm-v21.t2flow
+++ /dev/null
@@ -1,30875 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="dc6b1ade-a4eb-4032-af2a-689430f8438a" role="top"><name>Ecological_niche_mod</name><inputPorts><port><name>input_points</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
- <text>authorship,genusPart,infragenericEpithet,specificEpithet,infraspecificEpithet,nameComplete,uninomial,taxonName,occurrenceID,decimalLatitude,decimalLongitude,earliestDateCollected,latestDateCollected,coordinateUncertaintyInMeters,country,collector,fieldNotes,locality,maximumDepthInMeters,maximumElevationInMeters,minimumDepthInMeters,minimumElevationInMeters,value,dataProviderName,dataResourceName,dataResourceRights,dataResourceCitation,Column 28,Column 29
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784006,52.8951,4.7199,,,,NL,,,Koegras zuidelijk van camping Zwaluw.,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783531,51.4567,3.5655,,,,NL,,,"Menno v. Coehoorngracht - Vlissingen",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778754,51.8537,4.3301,,,,NL,,,Polderwatergang-gemaal Leeuw van Putten,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778454,52.5381,5.6766,,,,NL,,,RENDIERTOCHT ter hoogte van kavels K 37/,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789363,53.097,5.9827,,,,NL,,,"BOORNBERGUMERPETTEN, aanvoersloot 1",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783851,52.6594,5.9812,,,,NL,,,"KADOELERMEER - bij Kadoelersluis",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53776332,51.9121,4.1214,,,,NL,,,Inlaatwatering-langs de Dalweg te Oostvo,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53776237,52.4681,4.8064,,,,NL,,,"De Kogersluissloot - vanaf prov. weg",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53782072,52.732,4.8658,,,,NL,,,"Leyenpolderweg - ten zuiden van t V",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779042,51.6838,3.8394,,,,NL,,,"Flaauwers Inlaag - west",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787448,52.3064,5.0945,,,,NL,,,nieuwe keverdijkse polder,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779160,52.6751,4.7415,,,,NL,,,WATERSCHEIDING TUSSEN MIDDEN REKER- EN Z,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784254,52.5196,4.8814,,,,NL,,,"SLOOT TWEEDE SLOOT TOV BOERDERIJ HS N",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778851,53.3821,6.1796,,,,NL,,,Lauwersmeer Midden 2,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778229,51.5046,3.704,,,,NL,,,"Weel Suzannapolder - Arnemuiden",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789992,52.9031,5.47,,,,NL,,,"FLUESSEN - Galamadammen",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780927,52.5241,4.9623,,,,NL,,,"Sloot parallel aan Meeuwstraat - tpv loo",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780821,52.7862,4.8571,,,,NL,,,"Barsingerhorn - vaart Nzijde Dorpsstraat",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789316,52.5782,5.9497,,,,NL,,,Hoofdtocht Polder Koekoek,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53790117,52.7537,4.963,,,,NL,,,KLEIPUT ZUIDZIJDE WESTFRIESE DIJK 450 M,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787419,51.4567,3.5655,,,,NL,,,"Menno v. Coehoorngracht - Vlissingen",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778547,52.29,5.0211,,,,NL,,,"1.9km n Veltersloot PEN",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779121,52.8983,4.9392,,,,NL,,,"Westerland - thv rioolgemaal - nabij split",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789607,52.9051,5.0504,,,,NL,,,HOOGE KWELSLOOT KRUISING SLUITGATWEG,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784133,52.7322,5.1419,,,,NL,,,"NARREVLIET NOORDZIJDE VOKKOMMENWEG THV",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787081,52.4203,4.6714,,,,NL,,,BIJ GEMAAL TEN WESTEN VAN SPAARNDAM,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781688,52.9149,5.5534,,,,NL,,,"HET ZWIN -Oudega 2 toevoer",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780907,52.572,4.7471,,,,NL,,,Noordhollands Kanaal pontveer Akersloot,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53776376,51.8116,4.3068,,,,NL,,,hoofdwatergang-bij gemaal De Biersum/Sch,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781036,52.0009,4.2744,,,,NL,,,Oude en Nieuwe Broekpolder gemaal,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778324,52.7992,4.6939,,,,NL,,,"SLOOT TOV WESTERDUINWEG NOORDZIJDE PA",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778293,53.019,4.8036,,,,NL,,,toevoerkanaal gemaal Prins Hendrikpolder,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786744,52.0056,4.3975,,,,NL,,,"Zuidpld van Delfgauw - Ecoplas uitlaat",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781220,52.8342,4.8113,,,,NL,,,"Oudesluis - tpv brug tussen de Ruigweg en",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779200,52.5271,5.9158,,,,NL,,,Natuurgebied De Enk,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784321,52.2917,4.9313,,,,NL,,,OUDERKERKERPLAS MIDDEN OP DE PLAS,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786909,52.3024,5.1151,,,,NL,,,Naardermeer(Groote meer),,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784041,52.8432,5.5714,,,,NL,,,"poldervaart HUITEBUURSTERPOLDER - gemaal",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783983,52.9344,4.7627,,,,NL,,,"SLOOT HALF-GEISOL - TWV STATION DEN HELDE",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783445,52.2415,4.4736,,,,NL,,,Vogelsloot - t.O.v. Leeweg tussen weg en,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787106,52.2133,4.7239,,,,NL,,,Drecht t.h.v. de brug in Bilderdam,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779219,52.4276,5.0186,,,,NL,,,Bozen meertje,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783911,52.006,4.9585,,,,NL,,,eb13 Benschopperwetering brug huisnr. 32,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783572,52.8387,4.7211,,,,NL,,,"SLOOT BIJ DUIKER TNV KRUIS - UITLANDER",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778356,52.7451,4.7979,,,,NL,,,"Harenkarspel - waterb 400m N gem Woudmeer",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781528,52.0369,4.218,,,,NL,,,Oostmadeplas Loosduinen,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779249,52.0092,4.5539,,,,NL,,,Rottemeren-noord 1,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784337,52.0221,4.3797,,,,NL,,,Delftse Hout Grote plas,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778790,51.7836,4.3623,,,,NL,,,De Kreek,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783907,52.0221,4.3797,,,,NL,,,Delftse Hout Grote plas,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781976,51.6573,4.3615,,,,NL,,,Volkerak 2000,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787339,52.6978,5.2693,,,,NL,,,Grote Put te Enkhuizen,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789858,52.3378,4.5995,,,,NL,,,"Leidsetrekvaart vanaf brug in het manpa",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780981,52.382,4.7663,,,,NL,,,ZZ DUIKER IN KRUISING HOOFDSLOOT MET TOM,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787145,52.7537,4.8258,,,,NL,,,"SLOOT TZV MIDDENWEG 300 M TWV T-SPL",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780795,52.8384,4.7539,,,,NL,,,"N-H Kanaal - tpv vlotbrug te t Zand",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781715,52.8733,5.046,,,,NL,,,WATERKAAPTOCHT BIJ BRUG IN OOM KEESWEG,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780971,52.4175,4.8968,,,,NL,,,Sloot vanaf brug t.p.v. Zuideinde nr. 50,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781884,52.3593,4.9422,,,,NL,,,ringvaart molukkenstraat,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778215,51.5771,4.4975,,,,NL,,,Krampenloop KRA2,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786891,52.5196,4.8814,,,,NL,,,"SLOOT TWEEDE SLOOT TOV BOERDERIJ HS N",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784082,52.7829,4.881,,,,NL,,,"tpv brug - einde doodlopende weg naar gem",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784067,52.7954,4.7232,,,,NL,,,"Zijpe en Hazepolder - Ruigeweg ten zuiden",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53790080,52.8,4.9493,,,,NL,,,Westfriesche Vaart thv de Ulkeweg,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781963,51.9496,4.2664,,,,NL,,,Westgaag of Spartelvaart,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779073,53.4217,6.8744,,,,NL,,,Binnenbermsloot ten noorden van Spijkste,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781301,52.6736,4.7922,,,,NL,,,"SLOOT HOEK SPANJAARDDAM 650 M TZV NAU",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53782040,52.7876,4.8876,,,,NL,,,poldersloot 140 m zuid van gemaal.,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780779,52.9054,5.6288,,,,NL,,,"SLOTERMEER - Lytse Jerden",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781517,52.0623,4.7485,,,,NL,,,Reewijkse Hout,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783781,53.1387,5.9329,,,,NL,,,"OUDE VENEN 6-9-Med",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780846,52.7075,5.7475,,,,NL,,,ESPELERVAART eind Jupiterstraat,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781656,53.1293,5.8882,,,,NL,,,"OUDE VENEN 8-t Bil",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779361,53.1362,6.7164,,,,NL,,,"Wolfsbarge punt 2 - uitlaat geul",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779142,52.7454,4.8259,,,,NL,,,"Slootwaardpolder - poldersloot langs Ring",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786677,52.5304,4.7817,,,,NL,,,"Marken-binnen - t Meertje tpv steiger in",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789381,52.5994,4.623,,,,NL,,,"CASTRICUM EERSTE BOMTRECHTER TOV KRUIS",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786590,52.8043,4.6979,,,,NL,,,Sintmaarteszee.Wegsloot langs Westerduin,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778885,52.8805,4.7847,,,,NL,,,De Ballast noordelijk van duiker in Mole,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787171,52.6832,4.8616,,,,NL,,,OOSTERTOCHT KRUISING MOLENWEG,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778277,53.181,5.5055,,,,NL,,,"VAN HARINXMAKANAAL - Kiesterzijl",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780842,52.7244,4.6989,,,,NL,,,CATRIJPERMOOR DUIKER HOGE WEG ZUIDWESTZI,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784019,52.8733,5.046,,,,NL,,,WATERKAAPTOCHT BIJ BRUG IN OOM KEESWEG,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783927,51.8688,4.4999,,,,NL,,,Recreatieplas-Recreatieplas Zuidelijk Ra,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53782218,52.3653,4.6377,,,,NL,,,Zuider Buiten Spaarne ten zuiden van spo,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787091,52.397,4.9206,,,,NL,,,Florapark vijver,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778497,52.472,4.8625,,,,NL,,,NATUURBAD WIJDE WORMER VANAF STEIGER,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787513,52.8538,5.0491,,,,NL,,,"Oostertocht - tpv brug in de Robbenoordwe",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778439,52.5745,4.7172,,,,NL,,,"Laandervaart bij duiker in Rijksweg - km",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784296,52.4447,4.9826,,,,NL,,,TOEVOERSLOOT GEMAAL NOORDZIJDE DUIKER,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784536,52.8843,4.8755,,,,NL,,,"van Ewijcksvaart - brug te Ewijcksluis",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53776300,51.9778,4.459,,,,NL,,,Rodenrijse Vaart/Noordeindsevaart,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53783786,53.0701,4.778,,,,NL,,,Kopsloot Zuideinde v. effluentsloot bij,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784052,52.8258,5.0787,,,,NL,,,Hoekvaart tpv brug in de Schervenweg,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778266,53.2722,5.586,,,,NL,,,"HOLLE RIJ - langs Westerweg",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789719,52.5296,4.7274,,,,NL,,,Havens,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778391,52.6613,4.7457,,,,NL,,,"Noordhollands Kanaal - Koedijkervlotbrug",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53779158,52.6872,4.7948,,,,NL,,,Zuidelijke wegsloot v.d. Pieter Zeemanwe,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789477,52.4937,4.6964,,,,NL,,,"SLOOT NZ INSTEEKW - VANAF PARALLELWEG A 9",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778328,52.795,4.9319,,,,NL,,,"Groettocht - tpv brug in Kolhornerweg.",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778949,52.5202,4.839,,,,NL,,,"Wormer - Jisp & Neck- zijsloot van Noorde",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53781450,52.3324,5.2982,,,,NL,,,"HOGE VAART - brug Vogelweg",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53789398,51.8424,4.1314,,,,NL,,,Hoofdwatergang-Ossehoekweg west te Helle,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786572,52.8367,5.906,,,,NL,,,"ROTTIGE MEENTHE 8 - petgat zuid",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778374,52.7109,5.8671,,,,NL,,,"Stadsgracht Marknesse - kerkpad",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778515,52.4021,5.6786,,,,NL,,,Veluwemeer,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778723,51.9126,4.3173,,,,NL,,,Vlaardingen Heemtuin,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53784433,53.169,4.873,,,,NL,,,"T.p.v. afwateringsduiker - polder Wassena",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53787401,51.8654,4.4536,,,,NL,,,Hoofdwatergang-samenkomst Z.wegsloot van,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53778707,51.956,4.4984,,,,NL,,,Bergsche Voorplas,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53780848,52.694,5.9601,,,,NL,,,Vollenhovermeer de Voorst - AT000096,,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,
-,,,,,Gammarus tigrinus,,Gammarus tigrinus,53786596,52.7949,4.86,,,,NL,,,"PLAS NZ PROV - WEG STOLPEN-MIDDENMEER 300",,,,,,NLBIF,Limnodata,Copyright text.,IPR Text to be completed http://www.bgbm.org/disclaim_e.htm,,</text>
- </annotationBean>
- <date>2013-01-10 15:46:36.420 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This input takes a text file containing species occurrence points in CSV format. Each line in the file corresponds to a different record with values separated by comma. The first line must be a header containing column names also separated by comma. The following columns are mandatory to run this workflow AND must be spelled EXACTLY as follows: occurrenceID, nameComplete, decimalLongitude and decimalLatitude. Other columns can be present on the file. Columns can be in any order, but they must match the order of the corresponding values. All records are used to generate a single model regardless of the species name.</text>
- </annotationBean>
- <date>2013-11-29 11:04:37.943 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>serialized_final_model</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>The serialization of the model that was created with all points. This is an XML content specific to openModeller.</text>
- </annotationBean>
- <date>2013-01-09 11:32:46.865 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>create_final_model_log</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>The log from creating the final model. This is only output for information.</text>
- </annotationBean>
- <date>2013-01-09 11:44:01.956 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>internal_test_model_log</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>The log from testing the model. This is only output for information.</text>
- </annotationBean>
- <date>2011-11-24 14:22:44.267 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>internal_test_model_statistics</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>An XML document containing statistics for the result of the testing of the model.</text>
- </annotationBean>
- <date>2011-11-24 14:24:54.690 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>area_statistics</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>List of projection statistics as XML content returned from openModeller.</text>
- </annotationBean>
- <date>2013-01-09 11:48:15.378 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>projection_url</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>List of projected models as URLs from where the corresponding files can be downloaded.</text>
- </annotationBean>
- <date>2013-10-21 19:04:43.683 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>project_model_output_log</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>List of logs for each model projection.</text>
- </annotationBean>
- <date>2013-01-09 11:46:29.283 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>mean_auc</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>Mean AUC value of the external tests performed during cross validation.</text>
- </annotationBean>
- <date>2013-01-09 11:41:31.57 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>external_auc_list</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>List of AUCs that resulted from the cross validation.</text>
- </annotationBean>
- <date>2013-01-09 11:40:56.674 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>xval_create_model_log</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>A list of logs for each model creation during cross validation. One log for each replicate. This output is only expected to be used to give more details of an eventual problem during cross validation.</text>
- </annotationBean>
- <date>2013-01-09 11:38:18.22 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>xval_test_model_log</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>A list of logs for each external test during cross validation. One log for each replicate. This output is only expected to be used to give more details of an eventual problem during cross validation.</text>
- </annotationBean>
- <date>2013-01-09 11:38:45.962 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>xval_test_model_statistics</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>A list of test results (XML content specific to openModeller) created as part of the cross validation. One result for each replicate. This output is mainly expected to be used to give more details of an eventual problem during cross validation.</text>
- </annotationBean>
- <date>2013-01-09 11:39:41.170 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>answer</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This is here just for flow control - you can ignore this value.</text>
- </annotationBean>
- <date>2013-10-21 19:05:10.187 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>BioSTIF_csv_data_url</name><annotations /></port><port><name>BioSTIF_link</name><annotations /></port><port><name>xval_threshold</name><annotations /></port><port><name>mean_omission</name><annotations /></port><port><name>external_omission_list</name><annotations /></port></outputPorts><processors><processor><name>select_algorithm</name><inputPorts><port><name>algorithms_xml</name><depth>0</depth></port></inputPorts><outputPorts><port><name>algorithm_xml</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part displays interfaces so that users can select algorithm and parameter values.</text>
- </annotationBean>
- <date>2012-12-21 17:06:58.257 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="algorithms_xml" to="algorithms_xml" /></inputMap><outputMap><map from="algorithm_xml" to="algorithm_xml" /></outputMap><configBean encoding="dataflow"><dataflow ref="bf994d6b-fb81-4faf-bb68-4ae63d840ab3" /></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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="algorithms_xml" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>parse_input_points</name><inputPorts><port><name>csv_content</name><depth>0</depth></port></inputPorts><outputPorts><port><name>long_idx</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>lat_idx</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>id_idx</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>taxon_points</name><depth>0</depth><granularDept
h>0</granularDepth></port><port><name>first_taxon_name</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part is responsible for parsing the input points, determining column indexes and returning the records as a single string (same original format) without the header.</text>
- </annotationBean>
- <date>2012-12-21 14:09:07.538 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="csv_content" to="csv_content" /></inputMap><outputMap><map from="first_taxon_name" to="first_taxon_name" /><map from="id_idx" to="id_idx" /><map from="lat_idx" to="lat_idx" /><map from="taxon_points" to="taxon_points" /><map from="long_idx" to="long_idx" /></outputMap><configBean encoding="dataflow"><dataflow ref="5f0b203e-b807-48ac-9188-5d54b055fc9b" /></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.t
2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="csv_content" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>create_model</name><inputPorts><port><name>algorithm_xml</name><depth>0</depth></port><port><name>layers</name><depth>0</depth></port><port><name>mask_id</name><depth>0</depth></port><port><name>environmentally_unique</name><depth>0</depth></port><port><name>spatially_unique</name><depth>0</depth></port><port><name>species_label</name><depth>0</depth></port><port><name>srs</name><depth>0</depth></port><port><name>absen
ce_points_xml</name><depth>0</depth></port><port><name>presence_points_xml</name><depth>0</depth></port></inputPorts><outputPorts><port><name>model_xml</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>log</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>full_serialized_final_model</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part creates the XML configuration for model creation.</text>
- </annotationBean>
- <date>2012-12-21 17:11:25.20 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="algorithm_xml" to="algorithm_xml" /><map from="absence_points_xml" to="absence_points_xml" /><map from="presence_points_xml" to="presence_points_xml" /><map from="species_label" to="species_label" /><map from="mask_id" to="mask_id" /><map from="layers" to="layers" /><map from="srs" to="srs" /><map from="spatially_unique" to="spatially_unique" /><map from="environmentally_unique" to="environmentally_unique" /></inputMap><outputMap><map from="full_serialized_final_model" to="full_serialized_final_model" /><map from="model_xml" to="model_xml" /><map from="log" to="log" /></outputMap><configBean encoding="dataflow"><dataflow ref="14fa2d32-2f6f-4184-8503-f3fa44226117" /></configB
ean><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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="algorithm_xml" depth="0" /><port name="layers" depth="0" /><port name="mask_id" depth="0" /><port name="environmentally_unique" depth="0" /><port name="spatially_unique" depth="0" /><port name="species_label" depth="0" /><port name="srs" depth="0" /><port name="absence_points_xml" depth="0" /><port name="presence_points_xml" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>select_layers</name><inputPorts><port><name>om_layers_xml</name><depth>0</depth></port><port><name>biostif_l
ayers_xml_list</name><depth>1</depth></port></inputPorts><outputPorts><port><name>selected_layers_ids</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>selected_layers_labels</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part displays an interface so that users can select layers for model creation.</text>
- </annotationBean>
- <date>2012-12-21 17:09:08.627 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="biostif_layers_xml_list" to="biostif_layers_xml_list" /><map from="om_layers_xml" to="om_layers_xml" /></inputMap><outputMap><map from="selected_layers_ids" to="selected_layers_ids" /><map from="selected_layers_labels" to="selected_layers_labels" /></outputMap><configBean encoding="dataflow"><dataflow ref="c0584d3d-b17b-4ed5-9d65-3e6e0a5efd4b" /></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.workfl
owmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="om_layers_xml" depth="0" /><port name="biostif_layers_xml_list" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>test_model</name><inputPorts><port><name>layers</name><depth>0</depth></port><port><name>mask_id</name><depth>0</depth></port><port><name>calculate_roc</name><depth>0</depth></port><port><name>calculate_matrix</name><depth>0</depth></port><port><name>presence_points_xml</name><depth>0</depth></port><port><name>absence_points_xml</name><depth>0</depth></port><port><name
>srs</name><depth>0</depth></port><port><name>threshold</name><depth>0</depth></port><port><name>num_background_points</name><depth>0</depth></port><port><name>species_label</name><depth>0</depth></port><port><name>model_xml</name><depth>0</depth></port></inputPorts><outputPorts><port><name>test_statistics</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>log</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part is responsible for testing a model.</text>
- </annotationBean>
- <date>2013-10-15 14:52:39.817 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="calculate_matrix" to="calculate_matrix" /><map from="num_background_points" to="num_background_points" /><map from="absence_points_xml" to="absence_points_xml" /><map from="presence_points_xml" to="presence_points_xml" /><map from="species_label" to="species_label" /><map from="layers" to="layers" /><map from="mask_id" to="mask_id" /><map from="srs" to="srs" /><map from="model_xml" to="model_xml" /><map from="calculate_roc" to="calculate_roc" /><map from="threshold" to="threshold" /></inputMap><outputMap><map from="log" to="log" /><map from="test_statistics" to="test_statistics" /></outputMap><configBean encoding="dataflow"><dataflow ref="46a46f58-d176-40ab-a885-a1a189990812
" /></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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="layers" depth="0" /><port name="mask_id" depth="0" /><port name="calculate_roc" depth="0" /><port name="calculate_matrix" depth="0" /><port name="presence_points_xml" depth="0" /><port name="absence_points_xml" depth="0" /><port name="srs" depth="0" /><port name="threshold" depth="0" /><port name="num_background_points" depth="0" /><port name="species_label" depth="0" /><port name="model_xml" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>show_test_results</name><inputPorts><po
rt><name>statistics</name><depth>0</depth></port></inputPorts><outputPorts><port><name>answer</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part is responsible for showing the results of the internal test.</text>
- </annotationBean>
- <date>2012-12-21 17:20:08.438 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="statistics" to="statistics" /></inputMap><outputMap><map from="answer" to="answer" /></outputMap><configBean encoding="dataflow"><dataflow ref="ef4830ab-c0e3-40e1-8920-692b6752780c" /></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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="statistics" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>allocate_points</name><inputPorts><port><name>id_idx</name><depth>0</depth></port><port><name>long_idx</name><depth>0</depth></port><port><name>lat_idx</name><depth>0</depth></port><port><name>csv_points</name><depth>0</depth></port></inputPorts><outputPorts><port><name>all_points</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.
t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part is responsible for transforming the csv lines into a list of XML points. It returns a list of all points as well as two lists with 10 elements containig training and testing points to be used in 10-fold cross validation.</text>
- </annotationBean>
- <date>2012-12-21 17:05:07.152 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="csv_points" to="csv_points" /><map from="id_idx" to="id_idx" /><map from="lat_idx" to="lat_idx" /><map from="long_idx" to="long_idx" /></inputMap><outputMap><map from="all_points" to="all_points" /></outputMap><configBean encoding="dataflow"><dataflow ref="1bebe1f5-10ec-4647-97ad-77a1f30393af" /></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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="id_idx" depth="0" /><port name="long_idx" depth="0" /><port name="lat_idx" depth="0" /><port name="csv_points" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>run_cross_validation</name><inputPorts><port><name>layers_str</name><depth>0</depth></port><port><name>algorithm_xml</name><depth>0</depth></port><port><name>sentinel</name><depth>0</depth></port><port><name>mask</name><depth>0</depth></port><port><name>testing_points</name><depth>0</depth></port><port><name>training_point
s</name><depth>0</depth></port><port><name>calculate_matrix</name><depth>0</depth></port><port><name>measure_auc</name><depth>0</depth></port><port><name>threshold</name><depth>0</depth></port></inputPorts><outputPorts><port><name>xval_create_model_log</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>xval_test_model_statistics</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>xval_threshold</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>xval_test_model_log</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>xval_serialized_model</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part is responsible for performing 10-fold cross validation.</text>
- </annotationBean>
- <date>2012-12-21 17:22:28.216 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="calculate_matrix" to="calculate_matrix" /><map from="algorithm_xml" to="algorithm_xml" /><map from="measure_auc" to="measure_auc" /><map from="sentinel" to="sentinel" /><map from="training_points" to="training_points" /><map from="mask" to="mask" /><map from="layers_str" to="layers_str" /><map from="testing_points" to="testing_points" /><map from="threshold" to="threshold" /></inputMap><outputMap><map from="xval_create_model_log" to="xval_create_model_log" /><map from="xval_serialized_model" to="xval_serialized_model" /><map from="xval_test_model_log" to="xval_test_model_log" /><map from="xval_threshold" to="xval_threshold" /><map from="xval_test_model_statistics" to="xval_t
est_model_statistics" /></outputMap><configBean encoding="dataflow"><dataflow ref="9e243893-bafc-4e4c-ad04-9b11c0a81b1e" /></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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="layers_str" depth="0" /><port name="algorithm_xml" depth="0" /><port name="sentinel" depth="0" /><port name="mask" depth="0" /><dot><port name="training_points" depth="0" /><port name="testing_points" depth="0" /></dot><port name="calculate_matrix" depth="0" /><port name="measure_auc" depth="0" /><port name="threshold" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>extract_values</name><inputPorts><port><name>measure_auc</name><depth>0</depth></port><port><name>calculate_matrix
</name><depth>0</depth></port><port><name>test_statistics_xml</name><depth>0</depth></port></inputPorts><outputPorts><port><name>auc</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>omission</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part extracts the AUC value from all test results.</text>
- </annotationBean>
- <date>2012-12-21 17:24:11.379 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="test_statistics_xml" to="test_statistics_xml" /><map from="calculate_matrix" to="calculate_matrix" /><map from="measure_auc" to="measure_auc" /></inputMap><outputMap><map from="omission" to="omission" /><map from="auc" to="auc" /></outputMap><configBean encoding="dataflow"><dataflow ref="363aa707-3b0a-4fb4-8f5c-7556d7718efd" /></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.d
ispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="measure_auc" depth="0" /><port name="calculate_matrix" depth="0" /><port name="test_statistics_xml" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_AUC_List</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifa
ct><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>inputlist</name>
- <depth>2</depth>
- <mimeTypes>
- <string>l(l(''))</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>[B</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>
-</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>1.4</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>retrieve_algorithms</name><inputPorts /><outputPorts><port><name>algorithms_xml</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part is reponsible for retrieving all available algorithms from the niche modelling service.</text>
- </annotationBean>
- <date>2012-12-21 14:09:53.12 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap /><outputMap><map from="algorithms_xml" to="algorithms_xml" /></outputMap><configBean encoding="dataflow"><dataflow ref="bce215d0-4cf3-4f5e-9b48-d091f3427edd" /></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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>retrieve_layers</name><inputPorts /><outputPorts><port><name>om_layers_xml</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>biostif_layers_xml_list</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part is reponsible for retrieving all available layers from the niche modelling service and from the GeoServer repository at Fraunhofer.</text>
- </annotationBean>
- <date>2012-12-21 14:10:57.81 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap /><outputMap><map from="biostif_layers_xml_list" to="biostif_layers_xml_list" /><map from="om_layers_xml" to="om_layers_xml" /></outputMap><configBean encoding="dataflow"><dataflow ref="9a22d825-254d-4427-8137-d040d5c8b976" /></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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>input_mask_selection</name><inputPorts><port><name>selected_layers_labels</name><depth>0</depth></port><port><name>selected_layers_ids</name><depth>0</depth></port><port><name>om_layers_xml</name><depth>0</depth></port><port><name>biostif_layers_xml_list</name><depth>1</depth></port><port><name>csvDataURI</name><depth>0</depth></port></inputPorts><outputPorts><port><name>mask_id</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>created</name><depth>0</dept
h><granularDepth>0</granularDepth></port></outputPorts><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This part displays an interface so that users can select or create a mask for model creation.</text>
- </annotationBean>
- <date>2012-12-21 17:12:13.302 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="csvDataURI" to="csvDataURI" /><map from="selected_layers_ids" to="selected_layers_ids" /><map from="selected_layers_labels" to="selected_layers_labels" /><map from="biostif_layers_xml_list" to="biostif_layers_xml_list" /><map from="om_layers_xml" to="om_layers_xml" /></inputMap><outputMap><map from="created" to="created" /><map from="mask_id" to="mask_id" /></outputMap><configBean encoding="dataflow"><dataflow ref="b9efefb3-e015-4963-80af-3edf14b21ad3" /></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.work
flowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLaye
<TRUNCATED>
[9/9] incubator-taverna-language git commit: can't test enm workflow
Posted by st...@apache.org.
can't test enm workflow
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/3d74eb6e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/3d74eb6e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/3d74eb6e
Branch: refs/heads/master
Commit: 3d74eb6e29f56214ec1cf4ac75cacd6d6f0a7b55
Parents: 2f46d8d
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:39:11 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:39:11 2015 +0000
----------------------------------------------------------------------
.../scufl2/wfdesc/TestInvalidURITemplate.java | 94 --------------------
1 file changed, 94 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3d74eb6e/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestInvalidURITemplate.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestInvalidURITemplate.java b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestInvalidURITemplate.java
deleted file mode 100644
index c7e2161..0000000
--- a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestInvalidURITemplate.java
+++ /dev/null
@@ -1,94 +0,0 @@
-package org.apache.taverna.scufl2.wfdesc;
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.scufl2.api.io.ReaderException;
-import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
-import org.apache.taverna.scufl2.api.io.WriterException;
-import org.apache.taverna.scufl2.wfdesc.ROEvoSerializer;
-import org.junit.Before;
-import org.junit.Test;
-import org.openrdf.query.MalformedQueryException;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.QueryLanguage;
-import org.openrdf.repository.Repository;
-import org.openrdf.repository.RepositoryConnection;
-import org.openrdf.repository.RepositoryException;
-import org.openrdf.repository.sail.SailRepository;
-import org.openrdf.rio.RDFFormat;
-import org.openrdf.rio.RDFParseException;
-import org.openrdf.sail.memory.MemoryStore;
-
-
-public class TestInvalidURITemplate {
- private static final String ENM_v21 = "enm-v21.t2flow";
-
- ROEvoSerializer roEvo = new ROEvoSerializer();
- WorkflowBundleIO io = new WorkflowBundleIO();
-
- private WorkflowBundle localDependency;
-
- private ByteArrayOutputStream output = new ByteArrayOutputStream();
-
- @Before
- public void loadENM() throws ReaderException, IOException, WriterException, RDFParseException, RepositoryException, QueryEvaluationException, MalformedQueryException {
- InputStream localStream = getClass().getResourceAsStream("/" + ENM_v21);
- assertNotNull(localStream);
- localDependency = io.readBundle(localStream, "application/vnd.taverna.t2flow+xml");
- assertNotNull(localDependency);
- }
-
-
- @Test
- public void wfdesc() throws Exception {
- io.writeBundle(localDependency, output, "text/vnd.wf4ever.wfdesc+turtle");
-
- Repository myRepository = new SailRepository(new MemoryStore());
- myRepository.initialize();
- RepositoryConnection con = myRepository.getConnection();
- String root = "app:///";
- //System.out.write(output.toByteArray());
- con.add(new ByteArrayInputStream(output.toByteArray()), root, RDFFormat.TURTLE);
-
- assertFalse(con.prepareBooleanQuery(QueryLanguage.SPARQL,
- "PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#> " +
- "PREFIX wf4ever: <http://purl.org/wf4ever/wf4ever#> " +
- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " +
- "PREFIX roterms: <http://purl.org/wf4ever/roterms#> " +
- "ASK { " +
- "?ws a wfdesc:Process, wf4ever:RESTService ;" +
- " rdfs:label \"raster_upload_service\" ; " +
- " wf4ever:rootURI ?rootURI . " +
- "}").evaluate());
-
- }
-
-}
[3/9] incubator-taverna-language git commit: Remove MotifAnalysisIT
test
Posted by st...@apache.org.
Remove MotifAnalysisIT test
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/42eb15a3
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/42eb15a3
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/42eb15a3
Branch: refs/heads/master
Commit: 42eb15a386f02117585dedea76b96a7ea2239f55
Parents: a61518d
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:05:21 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:05:21 2015 +0000
----------------------------------------------------------------------
.../taverna/robundle/MotifAnalysisIT.java | 126 -------------------
1 file changed, 126 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/42eb15a3/taverna-robundle/src/test/java/org/apache/taverna/robundle/MotifAnalysisIT.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/MotifAnalysisIT.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/MotifAnalysisIT.java
deleted file mode 100644
index 54958b8..0000000
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/MotifAnalysisIT.java
+++ /dev/null
@@ -1,126 +0,0 @@
-package org.apache.taverna.robundle;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.net.URI;
-import java.nio.file.FileSystem;
-import java.nio.file.FileSystems;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.nio.file.StandardCopyOption;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.taverna.robundle.Bundle;
-import org.apache.taverna.robundle.Bundles;
-import org.apache.taverna.robundle.manifest.Agent;
-import org.apache.taverna.robundle.manifest.Manifest;
-import org.apache.taverna.robundle.manifest.PathAnnotation;
-import org.junit.Test;
-
-public class MotifAnalysisIT {
- @Test
- public void motifAnalysis() throws Exception {
-
- // The new RO bundle
- Path ro = Files.createTempFile("motifAnalysis", ".robundle.zip");
- try (Bundle bundle = Bundles.createBundle(ro)) {
-
- Path orig = Paths.get(getClass().getResource("/motifAnalysis.zip")
- .toURI());
-
- // Copy the motifAnalysis/ folder
- try (FileSystem origfs = FileSystems.newFileSystem(orig, null)) {
- Path origFolder = origfs.getPath("motifAnalysis/");
- Bundles.copyRecursively(origFolder, bundle.getRoot(),
- StandardCopyOption.REPLACE_EXISTING,
- StandardCopyOption.COPY_ATTRIBUTES);
- }
-
- // TODO: Generating manifest should be automatic!
-
- // Generate manifest
- Manifest manifest = bundle.getManifest();
-
- // attributions
-
- // Stian made the RO bundle
- Agent stian = new Agent();
- stian.setUri(URI.create("http://soiland-reyes.com/stian/#me"));
- stian.setOrcid(URI.create("http://orcid.org/0000-0001-9842-9718"));
- stian.setName("Stian Soiland-Reyes");
- manifest.setCreatedBy(stian);
- // RO bundle was created "now"
- manifest.setCreatedOn(Files.getLastModifiedTime(ro));
-
- // but it was *authored* by Daniel et al
-
- Agent daniel = new Agent();
- daniel.setUri(URI
- .create("http://delicias.dia.fi.upm.es/members/DGarijo/#me"));
- daniel.setOrcid(URI.create("http://orcid.org/0000-0003-0454-7145"));
- daniel.setName("Daniel Garijo");
-
- List<Agent> authors = new ArrayList<>();
- authors.add(daniel);
- authors.add(new Agent("Pinar Alper"));
- authors.add(new Agent("Khalid Belhajjame"));
- authors.add(new Agent("Oscar Corcho"));
- authors.add(new Agent("Yolanda Gil"));
- authors.add(new Agent("Carole Goble"));
- manifest.setAuthoredBy(authors);
-
- // when was the RO authored? We'll say when the README was made..
- Path readme = bundle.getRoot().resolve("README.txt");
- manifest.setAuthoredOn(Files.getLastModifiedTime(readme));
-
- // And who made the README file?
- manifest.getAggregation(readme).setCreatedBy(daniel);
- manifest.getAggregation(readme).setMediatype("text/plain");
-
- // Annotations
-
- PathAnnotation readmeAnnotation = new PathAnnotation();
- readmeAnnotation.setAbout(URI.create("/"));
- readmeAnnotation.setContent(URI.create("/README.txt"));
- readmeAnnotation.generateAnnotationId();
- manifest.getAnnotations().add(readmeAnnotation);
-
- PathAnnotation website = new PathAnnotation();
- website.setAbout(URI.create("/"));
- website.setContent(URI
- .create("http://www.oeg-upm.net/files/dgarijo/motifAnalysisSite/"));
- website.generateAnnotationId();
- manifest.getAnnotations().add(website);
-
- // Write out manifest
- // This is now done automatically on close()
- // manifest.writeAsJsonLD();
- }
-
- System.out.println("Generated " + ro);
- // if (Desktop.isDesktopSupported()) {
- // Desktop.getDesktop().open(ro.toFile());
- // }
- }
-
-}