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Posted to commits@taverna.apache.org by st...@apache.org on 2016/09/07 12:25:36 UTC
[2/2] incubator-taverna-plugin-bioinformatics git commit: Remove (c)
Edward Kawas, The BioMoby Project
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;