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Posted to commits@taverna.apache.org by st...@apache.org on 2016/09/07 12:25:35 UTC
[1/2] incubator-taverna-plugin-bioinformatics git commit: Avoid
duplicate ASF header
Repository: incubator-taverna-plugin-bioinformatics
Updated Branches:
refs/heads/master 314c60956 -> e3cd92036
Avoid duplicate ASF header
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/72c0785a
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/72c0785a
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/72c0785a
Branch: refs/heads/master
Commit: 72c0785affe69ff97acf6b72f4e6a376b4a11ccf
Parents: 314c609
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed Sep 7 13:23:05 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed Sep 7 13:23:05 2016 +0100
----------------------------------------------------------------------
taverna-biomoby-activity/pom.xml | 16 ----------------
1 file changed, 16 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/72c0785a/taverna-biomoby-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/pom.xml b/taverna-biomoby-activity/pom.xml
index 942b771..456f1a2 100644
--- a/taverna-biomoby-activity/pom.xml
+++ b/taverna-biomoby-activity/pom.xml
@@ -17,22 +17,6 @@
limitations under the 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.
--->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
[2/2] incubator-taverna-plugin-bioinformatics git commit: Remove (c)
Edward Kawas, The BioMoby Project
Posted by st...@apache.org.
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
Possibly an exception is CacheImpl which also says
(c) Martin Senger - I don't think we have ICLA for him.
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/e3cd9203
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/e3cd9203
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/e3cd9203
Branch: refs/heads/master
Commit: e3cd92036e8f04c416b414e8175ba633406b580d
Parents: 72c0785
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed Sep 7 13:23:28 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed Sep 7 13:25:28 2016 +0100
----------------------------------------------------------------------
NOTICE | 3 ++
.../biomoby/actions/AddParserActionHelper.java | 6 +---
.../BioMobyObjectTreeCustomRenderer.java | 5 ---
.../BioMobyServiceTreeCustomRenderer.java | 5 ---
.../biomoby/actions/BiomobyActionHelper.java | 6 +---
.../BiomobyActivityConfigurationAction.java | 4 ---
.../actions/BiomobyObjectActionHelper.java | 6 +---
.../biomoby/actions/BiomobyScavengerDialog.java | 29 ++++++---------
.../actions/MobyObjectDetailsAction.java | 3 --
.../biomoby/actions/MobyObjectTreeNode.java | 21 +++++------
.../activities/biomoby/actions/MobyPanel.java | 38 +++++++++-----------
.../biomoby/actions/MobyParserAction.java | 3 --
.../actions/MobyServiceDetailsAction.java | 4 ---
.../biomoby/actions/MobyServiceTreeNode.java | 17 ++++-----
.../biomoby/actions/SimpleActionFrame.java | 23 +++++-------
.../t2/activities/biomoby/query/CacheImpl.java | 25 ++++++-------
.../activities/biomoby/ui/DatatypeMenuItem.java | 5 ---
.../activities/biomoby/ExecuteCgiService.java | 4 ---
18 files changed, 65 insertions(+), 142 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/NOTICE
----------------------------------------------------------------------
diff --git a/NOTICE b/NOTICE
index a9f55c5..bc0df36 100644
--- a/NOTICE
+++ b/NOTICE
@@ -9,3 +9,6 @@ Portions of this software were originally based on the following:
These have been licensed to the Apache Software Foundation under a software grant.
---------------------------------------------------------
+TODO: taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
+says (c) Martin Senger and is licensed as LGPL - did University of Manchester
+have a ICLA from Senger so that this file can relicensed as Apache License?
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
index b03b98c..537dd8b 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.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.actions;
import java.awt.BorderLayout;
@@ -277,4 +273,4 @@ public class AddParserActionHelper {
private ImageIcon getIcon(String loc) {
return MobyPanel.getIcon(loc);
}
-}
\ No newline at end of file
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
index 46b4d5a..53384d9 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.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.actions;
import java.awt.Color;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
index ecce3ca..9d1b0c8 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.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.actions;
import java.awt.Color;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java
index 9579627..3270d35 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.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.actions;
import java.awt.BorderLayout;
@@ -849,4 +845,4 @@ public class BiomobyActionHelper {
newFrame.setVisible(true);
}
-}
\ No newline at end of file
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java
index f74c76a..36ce9ca 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.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.actions;
import java.awt.Frame;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.java
index 9ff9d67..e243a09 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.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.actions;
import java.awt.BorderLayout;
@@ -784,4 +780,4 @@ public class BiomobyObjectActionHelper {
public MobyNamespace[] getNamespaces() {
return this.namespaces == null ? new MobyNamespace[]{} : this.namespaces;
}
-}
\ No newline at end of file
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java
index 4419bf9..5c6ce8d 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java
@@ -1,12 +1,3 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-/*
- * 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.actions;
import java.awt.GridLayout;
@@ -29,7 +20,7 @@ import net.sf.taverna.t2.lang.ui.ShadedLabel;
/**
* a dialog for helping create scavengers for BioMoby registries that are not
* the default registry.
- *
+ *
*/
public class BiomobyScavengerDialog extends JPanel {
@@ -42,25 +33,25 @@ public class BiomobyScavengerDialog extends JPanel {
/**
* Default constructor.
- *
+ *
*/
/**
* Default constructor.
- *
+ *
*/
public BiomobyScavengerDialog() {
super();
GridLayout layout = new GridLayout(5, 2);
setLayout(layout);
-
+
registryEndpoint.setEnabled(false);
- registryURI.setEnabled(false);
-
+ registryURI.setEnabled(false);
+
// a combo box showing known registries
final Registries regs = RegistriesList.getInstance();
List<String> choices = new ArrayList<String>(Arrays.asList(regs.list()));
choices.add(CUSTOM);
-
+
JComboBox regList = new JComboBox(choices.toArray());
regList.setToolTipText("A selection will fill text fields below");
regList.setSelectedItem(Registries.DEFAULT_REGISTRY_SYNONYM);
@@ -75,7 +66,7 @@ public class BiomobyScavengerDialog extends JPanel {
return;
} else {
registryEndpoint.setEnabled(false);
- registryURI.setEnabled(false);
+ registryURI.setEnabled(false);
}
org.biomoby.registry.meta.Registry theReg = null;
try {
@@ -119,7 +110,7 @@ public class BiomobyScavengerDialog extends JPanel {
}
/**
- *
+ *
* @return the string representation of the BioMoby Registry endpoint
*/
public String getRegistryEndpoint() {
@@ -127,7 +118,7 @@ public class BiomobyScavengerDialog extends JPanel {
}
/**
- *
+ *
* @return the string representation of the BioMoby Registry endpoint
*/
public String getRegistryURI() {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
index 653571b..7195515 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
@@ -1,6 +1,3 @@
-/**
- *
- */
package net.sf.taverna.t2.activities.biomoby.actions;
import java.awt.Component;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java
index f58efc6..1aa2292 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java
@@ -1,23 +1,18 @@
-/*
- * 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.actions;
import org.biomoby.shared.MobyNamespace;
public class MobyObjectTreeNode {
-
+
// name of the object == node name
private String name = "";
-
+
// description of object == tool tip text
private String description = "";
-
+
private MobyNamespace[] ns = null;
/**
- *
+ *
* @param name - the name of the Moby Object
* @param description - the description of the Moby Service
*/
@@ -25,25 +20,25 @@ public class MobyObjectTreeNode {
this.name = name;
this.description = description;
}
- /*
+ /*
* over-ride the toString method in order to print node values
* that make sense.
*/
public String toString() {
return name;
}
-
+
public void setNamespaces(MobyNamespace[] namespaces) {
if (namespaces != null && namespaces.length == 0)
this.ns = null;
else
this.ns = namespaces;
}
-
+
public MobyNamespace[] getNamespaces() {
return this.ns;
}
-
+
public String getDescription() {
return this.description;
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java
index a2e0a70..455bf27 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java
@@ -1,9 +1,3 @@
-/*
- * Created on Sep 9, 2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
package net.sf.taverna.t2.activities.biomoby.actions;
import java.awt.BorderLayout;
@@ -21,17 +15,17 @@ import net.sf.taverna.t2.lang.ui.DialogTextArea;
/**
* @author Eddie Kawas
*
- *
+ *
*/
public class MobyPanel extends JPanel {
-
+
private static final long serialVersionUID = 1L;
private DialogTextArea textArea = null;
private String text = "";
private String name = "";
private JLabel jLabel = new JLabel();
-
+
/**
* This is the default constructor
*/
@@ -42,7 +36,7 @@ public class MobyPanel extends JPanel {
this.name = name;
initialize();
}
-
+
public MobyPanel(String label) {
super(new BorderLayout());
jLabel.setText(label);
@@ -50,7 +44,7 @@ public class MobyPanel extends JPanel {
}
/**
* This method initializes this
- *
+ *
* @return void
*/
private void initialize() {
@@ -61,10 +55,10 @@ public class MobyPanel extends JPanel {
}
/**
- * This method initializes jTextArea
- *
- * @return DialogTextArea
- */
+ * This method initializes jTextArea
+ *
+ * @return DialogTextArea
+ */
private DialogTextArea getTextArea() {
if (textArea == null) {
textArea = new DialogTextArea();
@@ -78,7 +72,7 @@ public class MobyPanel extends JPanel {
textArea.setCaretPosition(0);
return textArea;
}
-
+
public void setText(String text) {
this.text = text;
if (textArea == null) {
@@ -93,16 +87,16 @@ public class MobyPanel extends JPanel {
public ImageIcon getIcon() {
return new ImageIcon(MobyPanel.class.getResource("/moby_small.png"));
}
-
+
/**
- *
+ *
* @param icon a relative path to an icon to get
- * @return the ImageIcon at icon
+ * @return the ImageIcon at icon
*/
public static ImageIcon getIcon(String icon) {
return new ImageIcon(MobyPanel.class.getResource(icon));
}
-
+
public String getName(){
if (name==null) return "";
else return name;
@@ -110,12 +104,12 @@ public class MobyPanel extends JPanel {
public void onDisplay() {
// TODO Auto-generated method stub
-
+
}
public void onDispose() {
// TODO Auto-generated method stub
-
+
}
public static Frame CreateFrame(String title) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
index 283e933..f1f5b62 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
@@ -1,6 +1,3 @@
-/**
- *
- */
package net.sf.taverna.t2.activities.biomoby.actions;
import java.awt.Component;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.java
index 5000986..6ee403d 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.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.actions;
import java.awt.Component;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.java
index c957a1f..7c2c083 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.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.actions;
import java.util.ArrayList;
@@ -10,17 +5,17 @@ public class MobyServiceTreeNode {
// name of the service == node name
private String name = "";
-
+
// list of objects that service produces
@SuppressWarnings("unused")
private ArrayList<MobyObjectTreeNode> mobyObjectTreeNodes = null;
-
+
// description of object == tool tip text
private String description = "";
-
+
/**
- *
+ *
* @param name - the name of the Moby Service
* @param description - the description of the Moby Service
*/
@@ -28,14 +23,14 @@ public class MobyServiceTreeNode {
this.name = name;
this.description = description;
}
- /*
+ /*
* over-ride the toString method in order to print node values
* that make sense.
*/
public String toString() {
return name;
}
-
+
public String getDescription() {
return this.description;
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.java
index a85b50b..bee29da 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.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.actions;
import java.awt.BorderLayout;
@@ -14,33 +9,33 @@ import javax.swing.JPanel;
/**
* This class contains some methods that are useful in creating a consistent JPanel
* for displaying information or actions for biomoby services and datatypes.
- *
+ *
* @author Edward Kawas
* @author Stuart Owen = initial port from T1 to T2
- *
+ *
*/
public class SimpleActionFrame extends JPanel {
private static final long serialVersionUID = -6611234116434482238L;
-
-
+
+
private String name = "";
public SimpleActionFrame(Component c, String name) {
super(new BorderLayout());
add(c, BorderLayout.CENTER);
-
+
this.name = name;
}
-
+
public String getName() {
return name;
}
public void onDisplay() {
-
+
}
-
- }
\ No newline at end of file
+
+ }
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
index 37d677e..147f401 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
@@ -1,13 +1,8 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
/*
* This file is a component of the Taverna project,
* and is licensed under the GNU LGPL.
* Copyright Edward Kawas, Martin Senger, The BioMoby Project
*/
-
package net.sf.taverna.t2.activities.biomoby.query;
import java.io.BufferedOutputStream;
@@ -33,16 +28,16 @@ import org.biomoby.shared.MobyException;
* use the results of the cached cumulative results (their implementation is
* just passed to the parent class).
* <p>
- *
+ *
* The caching is done in the file system, not in memory, so the results are
* permanent (until someone removes the caching directory, or calls
* {@link #removeFromCache}).
* <p>
- *
+ *
* This class can be used also without caching - just instantiate it with
* 'cacheDir' set to null in the constructor.
* <p>
- *
+ *
* @author <A HREF="mailto:martin.senger@gmail.com">Martin Senger</A>
* @version $Id: CacheImpl.java,v 1.2 2008/09/04 13:42:16 sowen70 Exp $
*/
@@ -144,7 +139,7 @@ public class CacheImpl {
* Return a directory name representing the current cache. This is the same
* name as given in constructors.
* <p>
- *
+ *
* @return current cache directory name
**************************************************************************/
public String getCacheDir() {
@@ -156,7 +151,7 @@ public class CacheImpl {
* whole cache (for that Moby registry this instance was initiated for).
* Otherwise 'id' indicates which part of the cache that will be removed.
* <p>
- *
+ *
* @param id
* should be either null, or one of the following:
* {@link #CACHE_PART_DATATYPES}, {@link #CACHE_PART_SERVICES},
@@ -186,7 +181,7 @@ public class CacheImpl {
* Create a cache directory from 'cacheDirectory' and 'registryId' if it
* does not exist yet. Make sure that it is writable. Return a File
* representing created directory.
- *
+ *
* 'registryId' (which may be null) denotes what registry this cache is
* going to be created for. If null, an endpoint of a default Moby registry
* is used.
@@ -348,7 +343,7 @@ public class CacheImpl {
urlConnection.setUseCaches(false);
urlConnection.setRequestProperty ( "User-agent", "Taverna_BioMOBY/1.5");
urlConnection.setConnectTimeout(1000*60*5);
-
+
BufferedReader in = new BufferedReader(new InputStreamReader(
urlConnection.getInputStream()));
String inputLine;
@@ -468,7 +463,7 @@ public class CacheImpl {
}
/***************************************************************************
- *
+ *
**************************************************************************/
protected static String MSG_CACHE_NOT_DIR(File cache) {
return "Surprisingly, '" + cache.getAbsolutePath()
@@ -476,7 +471,7 @@ public class CacheImpl {
}
/***************************************************************************
- *
+ *
**************************************************************************/
protected static String MSG_CACHE_BAD_FILE(File file, Exception e) {
return "Ignoring '" + file.getPath()
@@ -488,7 +483,7 @@ public class CacheImpl {
* Return age of the current (whole) cache in millis from the beginning of
* the Epoch; or -1 if cache is empty, or the age is unknown.
* <p>
- *
+ *
* @return the cache age which is taken as the oldest (but filled) cache
* part (part is considered e.g. 'services', or 'data types', not
* their individual entities)
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e3cd9203/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
index c5a7468..6002a4d 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.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/e3cd9203/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java
index d66263c..bf28606 100644
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java
+++ b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java
@@ -20,10 +20,6 @@ package net.sf.taverna.t2.activities.biomoby;
import java.io.BufferedReader;
import java.io.InputStreamReader;
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
import java.io.OutputStreamWriter;
import java.net.URL;
import java.net.URLConnection;