Repository: incubator-taverna-plugin-bioinformatics Updated Branches: refs/heads/master e3cd92036 -> 6adfc5bfe
Remove (c) Edward Kawas, The BioMoby Project Kawas signed ICLA with Univ of Manchester, and these files were further part of the Software Grant to ASF filed 2015-02-23. They can therefore be relicensed as Apache License 2.0 Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/commit/6adfc5bf Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/6adfc5bf Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/6adfc5bf Branch: refs/heads/master Commit: 6adfc5bfee340c304592dc3aa32e7ea2fe8a0c8c Parents: e3cd920 Author: Stian Soiland-Reyes <[email protected]> Authored: Wed Sep 7 13:27:01 2016 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Wed Sep 7 13:27:01 2016 +0100 ---------------------------------------------------------------------- .../biomoby/edits/AddBiomobyDataTypeEdit.java | 4 ---- .../biomoby/query/BiomobyActivityIcon.java | 4 ---- .../biomoby/query/BiomobyActivityItem.java | 4 ---- .../biomoby/query/BiomobyObjectActivityIcon.java | 4 ---- .../biomoby/query/BiomobyObjectActivityItem.java | 4 ---- .../biomoby/query/BiomobyQueryHelper.java | 18 +++++++----------- .../activities/biomoby/ui/BiomobyObjectTree.java | 5 ----- .../view/BiomobyActivityContextualView.java | 4 ---- .../BiomobyActivityContextualViewFactory.java | 4 ---- .../view/BiomobyContextualViewFactoryTest.java | 4 ---- 10 files changed, 7 insertions(+), 48 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyDataTypeEdit.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyDataTypeEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyDataTypeEdit.java index e13c264..739f503 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyDataTypeEdit.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyDataTypeEdit.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.edits; import java.util.ArrayList; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java index 2c28c32..5b2106a 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.query; import javax.swing.Icon; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java index a799280..e5fb5c4 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.query; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java index f4575e4..aca7cf7 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.query; import javax.swing.Icon; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java index 1e50d37..5c96869 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.query; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java index e22b78c..6447393 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.query; import java.io.File; @@ -50,7 +46,7 @@ public class BiomobyQueryHelper { private String remoteServiceRdfUrl = null; private static final String CACHE_NAME = "moby-cache"; - + private ApplicationRuntime applicationRuntime = ApplicationRuntime .getInstance(); @@ -80,7 +76,7 @@ public class BiomobyQueryHelper { this.registryNamespace, cacheLoc + CACHE_NAME); } catch (MobyException e) { - // + // log.warn("There was a problem in initializing the caching agent, therefor caching is disabled.", e); } @@ -96,7 +92,7 @@ public class BiomobyQueryHelper { } /** - * + * * @return an ArrayList of BiomobyActivityItem * @throws MobyException * if something goes wrong @@ -221,19 +217,19 @@ public class BiomobyQueryHelper { callBack.partialResults(findDatatypeDescriptions()); callBack.finished(); } - + public List<BiomobyDatatypeDescription> findDatatypeDescriptions() { try { central.updateCache(CentralDigestCachedImpl.CACHE_PART_DATATYPES); } catch (MobyException ex) { - + return new ArrayList<BiomobyDatatypeDescription>(); } MobyDataType[] datatypes; try { datatypes = central.getDataTypes(); } catch (MobyException ex) { - + return new ArrayList<BiomobyDatatypeDescription>(); } List<BiomobyDatatypeDescription> datatypeDescriptions = new ArrayList<BiomobyDatatypeDescription>(); @@ -251,7 +247,7 @@ public class BiomobyQueryHelper { try { dataDesc.setLsid(URI.create(lsid)); } catch (Exception e) { - + } } ArrayList<String> lineage = new ArrayList<String>(); http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java index 7ca2578..52622cd 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java @@ -1,8 +1,3 @@ -/* - * This file is a component of the Taverna project, - * and is licensed under the GNU LGPL. - * Copyright Edward Kawas, The BioMoby Project - */ package net.sf.taverna.t2.activities.biomoby.ui; import java.awt.BorderLayout; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java index 4911721..d64634a 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.view; import java.awt.BorderLayout; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java index 942e52c..24c9a5d 100644 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.view; import java.util.Arrays; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/6adfc5bf/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java b/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java index a9c51c6..1e18b80 100644 --- a/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java +++ b/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java @@ -1,7 +1,3 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ package net.sf.taverna.t2.activities.biomoby.view; import static org.junit.Assert.assertNull;
