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 <[email protected]> Authored: Wed Sep 7 13:23:28 2016 +0100 Committer: Stian Soiland-Reyes <[email protected]> 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:[email protected]";>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;
