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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:47:08 UTC
[41/50] [abbrv] incubator-taverna-plugin-bioinformatics git commit:
taverna-soaplab-activity-ui/
taverna-soaplab-activity-ui/
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/418e332b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/418e332b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/418e332b
Branch: refs/heads/master
Commit: 418e332ba99914b85fe167d3022bb4f4cbc0c7c1
Parents: 215bd93
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Feb 2 09:50:18 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Feb 2 09:55:09 2015 +0000
----------------------------------------------------------------------
.gitignore | 24 ---
.travis.yml | 1 -
README.md | 5 -
pom.xml | 103 -----------
.../SoaplabActivityConfigurationAction.java | 68 -------
.../actions/SoaplabConfigurationPanel.java | 183 -------------------
.../ConfigureSoaplabActivityMenuAction.java | 54 ------
.../MissingSoaplabException.java | 63 -------
.../SoaplabActivityIcon.java | 60 ------
.../servicedescriptions/SoaplabCategory.java | 80 --------
.../SoaplabScavengerAgent.java | 144 ---------------
.../SoaplabServiceDescription.java | 131 -------------
.../SoaplabServiceProvider.java | 183 -------------------
.../SoaplabServiceProviderConfig.java | 38 ----
.../views/SoaplabActivityContextualView.java | 156 ----------------
.../views/SoaplabActivityViewFactory.java | 73 --------
...rvicedescriptions.ServiceDescriptionProvider | 1 -
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 -
...a.t2.workbench.activityicons.ActivityIconSPI | 1 -
...ntextualviews.activity.ContextualViewFactory | 1 -
.../spring/soaplab-activity-ui-context-osgi.xml | 28 ---
.../spring/soaplab-activity-ui-context.xml | 27 ---
src/main/resources/analysis_metadata_2_html.xsl | 96 ----------
src/main/resources/soaplab.png | Bin 701 -> 0 bytes
.../TestSoaplabActivityContextualView.java | 61 -------
taverna-soaplab-activity-ui/pom.xml | 103 +++++++++++
.../SoaplabActivityConfigurationAction.java | 68 +++++++
.../actions/SoaplabConfigurationPanel.java | 183 +++++++++++++++++++
.../ConfigureSoaplabActivityMenuAction.java | 54 ++++++
.../MissingSoaplabException.java | 63 +++++++
.../SoaplabActivityIcon.java | 60 ++++++
.../servicedescriptions/SoaplabCategory.java | 80 ++++++++
.../SoaplabScavengerAgent.java | 144 +++++++++++++++
.../SoaplabServiceDescription.java | 131 +++++++++++++
.../SoaplabServiceProvider.java | 183 +++++++++++++++++++
.../SoaplabServiceProviderConfig.java | 38 ++++
.../views/SoaplabActivityContextualView.java | 156 ++++++++++++++++
.../views/SoaplabActivityViewFactory.java | 73 ++++++++
...rvicedescriptions.ServiceDescriptionProvider | 1 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 +
...a.t2.workbench.activityicons.ActivityIconSPI | 1 +
...ntextualviews.activity.ContextualViewFactory | 1 +
.../spring/soaplab-activity-ui-context-osgi.xml | 28 +++
.../spring/soaplab-activity-ui-context.xml | 27 +++
.../main/resources/analysis_metadata_2_html.xsl | 96 ++++++++++
.../src/main/resources/soaplab.png | Bin 0 -> 701 bytes
.../TestSoaplabActivityContextualView.java | 61 +++++++
47 files changed, 1552 insertions(+), 1582 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index ebe0e5b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,24 +0,0 @@
-# ignore project files #
-.classpath
-.project
-.settings/
-catalog-v001.xml
-
-# ignore target files #
-target/
-bin/
-build/
-dist/
-apidoc/
-*.swp
-
-# ignore svn files if there
-.svn
-
-# ignore log files #
-*.log
-/logs/*
-*/logs/*
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index 349d824..0000000
--- a/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-Taverna Workflow system SoapLab Activity: User Interface part for use in the Taverna Workbench.
-
-Extends https://github.com/taverna/taverna-soaplab-activity
-
-This code was previously hosted at http://taverna.googlecode.com/svn/taverna/ui/net.sf.taverna.t2.ui-activities/
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 737a13d..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,103 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<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>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>soaplab-activity-ui</artifactId>
- <version>2.0-SNAPSHOT</version>
- <packaging>bundle</packaging>
- <name>Taverna 2 Soaplab Activity UI</name>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>soaplab-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-icons-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-palette-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>contextual-views-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-tools</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>edits-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>file-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>menu-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.apache.axis</groupId>
- <artifactId>com.springsource.org.apache.axis</artifactId>
- <version>${axis.version}</version>
- </dependency>
- <dependency>
- <groupId>javax.xml.rpc</groupId>
- <artifactId>com.springsource.javax.xml.rpc</artifactId>
- <version>${xml.rpc.version}</version>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository
- </url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-soaplab-activity-ui.git</connection>
- <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-soaplab-activity-ui.git</developerConnection>
- <url>https://github.com/taverna/taverna-soaplab-activity-ui/</url>
- <tag>HEAD</tag>
- </scm>
-
-</project>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
deleted file mode 100644
index 43b87f1..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.actions;
-
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class SoaplabActivityConfigurationAction extends ActivityConfigurationAction {
-
- private static final long serialVersionUID = 5076721332542691094L;
- private final Frame owner;
- public static final String CONFIGURE_SOAPLAB_ACTIVITY = "Configure Soaplab";
- private final EditManager editManager;
- private final FileManager fileManager;
-
- public SoaplabActivityConfigurationAction(Activity activity, Frame owner,
- EditManager editManager, FileManager fileManager,
- ActivityIconManager activityIconManager, ServiceDescriptionRegistry serviceDescriptionRegistry) {
- super(activity, activityIconManager, serviceDescriptionRegistry);
- this.editManager = editManager;
- this.fileManager = fileManager;
- putValue(Action.NAME, CONFIGURE_SOAPLAB_ACTIVITY);
- this.owner = owner;
- }
-
- public void actionPerformed(ActionEvent action) {
- ActivityConfigurationDialog currentDialog = ActivityConfigurationAction.getDialog(getActivity());
- if (currentDialog != null) {
- currentDialog.toFront();
- return;
- }
-
- final SoaplabConfigurationPanel panel = new SoaplabConfigurationPanel(getActivity());
- final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(
- getActivity(), panel, editManager);
-
- ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
deleted file mode 100644
index 9b4b0c8..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
+++ /dev/null
@@ -1,183 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.actions;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.JCheckBox;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.border.TitledBorder;
-
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-@SuppressWarnings("serial")
-public class SoaplabConfigurationPanel extends ActivityConfigurationPanel {
-
-// ActionListener closeClicked;
-// ActionListener applyClicked;
-
- private JTextField intervalMaxField;
- private JTextField intervalField;
- private JTextField backoffField;
- private JCheckBox allowPolling;
-
- public SoaplabConfigurationPanel(Activity activity) {
- super(activity);
- initialise();
- }
-
- public boolean isAllowPolling() {
- return allowPolling.isSelected();
- }
-
- public int getInterval() {
- return Integer.parseInt(intervalField.getText());
- }
-
- public int getIntervalMax() {
- return Integer.parseInt(intervalMaxField.getText());
- }
-
- public double getBackoff() {
- return Double.parseDouble(backoffField.getText());
- }
-
- @Override
- protected void initialise() {
- super.initialise();
- removeAll();
-
- setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
-
- JPanel interval = new JPanel();
- interval.setLayout(new BorderLayout());
- interval.setBorder(new TitledBorder("Interval"));
-
- JPanel intervalMax = new JPanel();
- intervalMax.setLayout(new BorderLayout());
- intervalMax.setBorder(new TitledBorder("Max interval"));
-
- JPanel backoff = new JPanel();
- backoff.setLayout(new BorderLayout());
- backoff.setBorder(new TitledBorder("Backoff"));
-
- intervalField = new JTextField(getJson().get("pollingInterval").asText());
- intervalMaxField = new JTextField(getJson().get("pollingIntervalMax").asText());
- backoffField = new JTextField(getJson().get("pollingBackoff").asText());
-
- interval.add(intervalField, BorderLayout.CENTER);
- intervalMax.add(intervalMaxField);
- backoff.add(backoffField);
-
- allowPolling = new JCheckBox("Polling?", getJson().get("pollingInterval").intValue() != 0);
- allowPolling.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- updateEnableForPollingFlag();
- }
- });
-
- updateEnableForPollingFlag();
- JPanel allowPollingPanel = new JPanel();
- allowPollingPanel.setLayout(new BorderLayout());
- allowPollingPanel.add(allowPolling, BorderLayout.WEST);
- add(allowPollingPanel);
- add(interval);
- add(intervalMax);
- add(backoff);
- add(Box.createGlue());
- validate();
- }
-
- @Override
- public void noteConfiguration() {
- if (validateValues()) {
- int interval = 0;
- int intervalMax = 0;
- double backoff = 1.1;
-
- if (isAllowPolling()) {
- interval = getInterval();
- intervalMax = getIntervalMax();
- backoff = getBackoff();
- }
-
- getJson().put("pollingBackoff", backoff);
- getJson().put("pollingInterval", interval);
- getJson().put("pollingIntervalMax", intervalMax);
- }
- }
-
- @Override
- public boolean checkValues() {
- // TODO Not yet implemented
- return true;
- }
-
- private void updateEnableForPollingFlag() {
- boolean enabled = allowPolling.isSelected();
- intervalField.setEnabled(enabled);
- intervalMaxField.setEnabled(enabled);
- backoffField.setEnabled(enabled);
- }
-
- public boolean validateValues() {
- if (allowPolling.isSelected()) {
- try {
- new Integer(intervalField.getText());
- } catch (Exception e) {
- JOptionPane.showMessageDialog(null, "The interval field must be a valid integer",
- "Invalid value", JOptionPane.ERROR_MESSAGE);
- return false;
-
- }
-
- try {
- new Integer(intervalMaxField.getText());
- } catch (Exception e) {
- JOptionPane.showMessageDialog(null,
- "The maximum interval field must be a valid integer", "Invalid value",
- JOptionPane.ERROR_MESSAGE);
- return false;
-
- }
-
- try {
- new Double(backoffField.getText());
- } catch (Exception e) {
- JOptionPane.showMessageDialog(null, "The backoff field must be a valid float",
- "Invalid value", JOptionPane.ERROR_MESSAGE);
- return false;
-
- }
- }
-
- return true;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/menu/ConfigureSoaplabActivityMenuAction.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/menu/ConfigureSoaplabActivityMenuAction.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/menu/ConfigureSoaplabActivityMenuAction.java
deleted file mode 100644
index f182ecb..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/menu/ConfigureSoaplabActivityMenuAction.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package net.sf.taverna.t2.activities.soaplab.menu;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.soaplab.actions.SoaplabActivityConfigurationAction;
-import net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
-import net.sf.taverna.t2.ui.menu.MenuComponent;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-
-public class ConfigureSoaplabActivityMenuAction extends AbstractConfigureActivityMenuAction
- implements MenuComponent, ContextualMenuComponent {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public ConfigureSoaplabActivityMenuAction() {
- super(SoaplabServiceDescription.ACTIVITY_TYPE);
- }
-
- @Override
- protected Action createAction() {
- SoaplabActivityConfigurationAction configAction = new SoaplabActivityConfigurationAction(
- findActivity(), getParentFrame(), editManager, fileManager, activityIconManager,
- serviceDescriptionRegistry);
- configAction.putValue(Action.NAME,
- SoaplabActivityConfigurationAction.CONFIGURE_SOAPLAB_ACTIVITY);
- addMenuDots(configAction);
- return configAction;
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
deleted file mode 100644
index 594a7a2..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MissingSoaplabException.java,v $
- * Revision $Revision: 1.3 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/11/19 17:33:04 $
- * by $Author: anenadic $
- * Created on 4 Sep 2006
- *****************************************************************/
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-@SuppressWarnings("serial")
-public class MissingSoaplabException extends Exception {
-
- public MissingSoaplabException(String msg) {
- super(msg);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
deleted file mode 100644
index f9d273b..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.net.URI;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
-
-/**
- *
- * @author Alex Nenadic
- *
- */
-public class SoaplabActivityIcon implements ActivityIconSPI{
-
- private static Icon icon;
-
- public int canProvideIconScore(URI activityType) {
- if (SoaplabServiceDescription.ACTIVITY_TYPE.equals(activityType))
- return DEFAULT_ICON + 1;
- else
- return NO_ICON;
- }
-
- public Icon getIcon(URI activityType) {
- return getSoaplabIcon();
- }
-
- public static Icon getSoaplabIcon() {
- if (icon == null) {
- icon = new ImageIcon(SoaplabActivityIcon.class
- .getResource("/soaplab.png"));
- }
- return icon;
- }
-
-}
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
deleted file mode 100644
index 47f994c..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: SoaplabCategory.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/09/04 13:40:38 $
- * by $Author: sowen70 $
- * Created on 4 Sep 2006
- *****************************************************************/
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.util.ArrayList;
-import java.util.List;
-
-public class SoaplabCategory {
-
- private String category;
- private List<String> services = new ArrayList<String>();
-
- public SoaplabCategory(String category) {
- this.category=category;
- }
-
- public boolean addService(String service) {
- return services.add(service);
- }
-
- public String getCategory() {
- return category;
- }
-
- public List<String> getServices() {
- return services;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
deleted file mode 100644
index fe428ec..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
+++ /dev/null
@@ -1,144 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: SoaplabScavengerAgent.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/09/04 13:40:37 $
- * by $Author: sowen70 $
- * Created on 4 Sep 2006
- *****************************************************************/
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.rmi.RemoteException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.rpc.ServiceException;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.log4j.Logger;
-
-/**
- * An agent to query Soaplab server to determine the available categories and services.
- * @author sowen
- *
- */
-
-public class SoaplabScavengerAgent {
-
- private static Logger logger = Logger.getLogger(SoaplabScavengerAgent.class);
-
- /**
- * Returns a list of soaplab categories, containing a list of their services.
- * Throws MissingSoaplabException if an installation cannot be found.
- */
- public static List<SoaplabCategory> load(String base) throws MissingSoaplabException{
- List<SoaplabCategory> categories=new ArrayList<SoaplabCategory>();
-
- // Get the categories for this installation
- boolean foundAnInstallation = loadCategories(base + "AnalysisFactory",categories);
-
- // Yes, bitwise OR is on purpose, to make sure the second
- // loadCategories() is always run. Do NOT replace with
- // foundInstallation = foundInstallation || getCategories(..)
- foundAnInstallation |= loadCategories(base + "GowlabFactory",categories);
- if (!foundAnInstallation) {
- // Neither Soaplab nor Gowlab were found, probably a fault
- throw new MissingSoaplabException("Unable to locate a soaplab installation at \n" + base);
- }
-
- return categories;
-
- }
-
-
- private static boolean loadCategories(String categoryBase, List<SoaplabCategory>cats) {
- boolean foundSome = false;
- String[] categories;
- try {
- categories = (String[]) callWebService(categoryBase, "getAvailableCategories", new Object[0]);
- } catch (Exception e) {
- logger.debug("Missing category: "+categoryBase, e);
- return false;
- }
- // Iterate over all the categories, creating new child nodes
- for (int i = 0; i < categories.length; i++) {
- String[] services;
- try {
- services = (String[]) callWebService(categoryBase, "getAvailableAnalysesInCategory", new Object[] {categories[i]});
- } catch (Exception e) {
- logger.info("Skipping category " + categories[i], e);
- continue;
- }
- if (services.length == 0) {
- // Avoid creating empty treenodes
- continue;
- }
-
- SoaplabCategory category=new SoaplabCategory(categories[i]);
- cats.add(category);
-
- foundSome = true;
- // Iterate over the services
- for (int j = 0; j < services.length; j++) {
- category.addService(services[j]);
- }
- }
- return foundSome;
- }
-
- public static Object callWebService(String target, String operation,
- Object[] parameters) throws ServiceException, RemoteException {
- Service service = new Service();
- Call call = (Call) service.createCall();
- call.setTargetEndpointAddress(target);
- // No need to do new Qname(operation) with unspecified namespaces
- call.setOperationName(operation);
- return call.invoke(parameters);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceDescription.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceDescription.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceDescription.java
deleted file mode 100644
index 99a25b3..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceDescription.java
+++ /dev/null
@@ -1,131 +0,0 @@
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-public class SoaplabServiceDescription extends ServiceDescription {
-
- public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/soaplab");
-
- private final static String SOAPLAB = "Soaplab @ ";
-
- private String category;
- private String operation;
- private URI endpoint;
- private List<String> types;
-
- private String name;
-
- public List<String> getTypes() {
- return types;
- }
-
- /**
- * @return the category
- */
- public String getCategory() {
- return category;
- }
-
- /**
- * @param category
- * the category to set
- */
- public void setCategory(String category) {
- this.category = category;
- }
-
- /**
- * @return the operation
- */
- public String getOperation() {
- return operation;
- }
-
- /**
- * @param operation
- * the operation to set
- */
- public void setOperation(final String operation) {
- this.operation = operation;
-
- String name = operation;
- int finalColon = operation.lastIndexOf(":");
- if (finalColon != -1) {
- name = operation.substring(finalColon + 1);
- }
- int finalDot = operation.lastIndexOf(".");
- if (finalDot != -1) {
- name = operation.substring(finalDot + 1);
- }
- setName(name);
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
-
- @Override
- public URI getActivityType() {
- return ACTIVITY_TYPE;
- }
-
- @Override
- public Configuration getActivityConfiguration() {
- Configuration configuration = new Configuration();
- configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
- ((ObjectNode) configuration.getJson()).put("endpoint", getEndpoint().toASCIIString() + getOperation());
- ((ObjectNode) configuration.getJson()).put("pollingInterval", 0);
- ((ObjectNode) configuration.getJson()).put("pollingBackoff", 1.0);
- ((ObjectNode) configuration.getJson()).put("pollingIntervalMax", 0);
- return configuration;
- }
-
- @Override
- public Icon getIcon() {
- return SoaplabActivityIcon.getSoaplabIcon();
- }
-
- @Override
- public String getName() {
- return name;
- }
-
- @Override
- public List<String> getPath() {
- List<String> path = new ArrayList<String>();
- path.add(SOAPLAB + getEndpoint());
- path.add(getCategory());
- // Don't use getTypes() - as we end up
- // with double entries..
- return path;
- }
-
- public void setTypes(List<String> types) {
- this.types = types;
- }
-
- public void setEndpoint(URI endpoint) {
- this.endpoint = endpoint;
- }
-
- public URI getEndpoint() {
- return endpoint;
- }
-
- @Override
- protected List<Object> getIdentifyingData() {
- return Arrays.<Object>asList(getEndpoint(), getOperation());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProvider.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProvider.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProvider.java
deleted file mode 100644
index 54080c9..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProvider.java
+++ /dev/null
@@ -1,183 +0,0 @@
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.net.URI;
-import java.rmi.RemoteException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.Icon;
-import javax.xml.rpc.ServiceException;
-
-import net.sf.taverna.t2.activities.soaplab.Soap;
-import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-
-import org.apache.log4j.Logger;
-
-public class SoaplabServiceProvider extends
- AbstractConfigurableServiceProvider<SoaplabServiceProviderConfig> {
-
- // To avoid hammering the soaplab service
- private static final int DELAY_MS = 100;
- private static final int DESCRIPTION_UPDATE_INTERVAL_MS = 2000;
-
- private static Logger logger = Logger
- .getLogger(SoaplabServiceProvider.class);
-
- private static final String SOAPLAB_SERVICE = "Soaplab service";
- private static final boolean FIND_DETAILS = false;
-
- private static final URI providerId = URI
- .create("http://taverna.sf.net/2010/service-provider/soaplab");
-
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public SoaplabServiceProvider() {
- super(new SoaplabServiceProviderConfig(
- "http://somehost/soaplab/services/"));
- }
-
- public void findServiceDescriptionsAsync(
- FindServiceDescriptionsCallBack callBack) {
- List<SoaplabServiceDescription> descriptions = findSoaplabServices(callBack);
- if (descriptions == null) {
- return;
- }
- callBack.partialResults(descriptions);
-
- if (FIND_DETAILS) {
- if (findSoaplabDetails(descriptions, callBack)) {
- callBack.finished();
- }
- } else {
- callBack.finished();
- }
- }
-
- public List<SoaplabServiceProviderConfig> getDefaultConfigurations() {
-
- List<SoaplabServiceProviderConfig> defaults = new ArrayList<SoaplabServiceProviderConfig>();
-
- // If defaults have failed to load from a configuration file then load them here.
- if (!serviceDescriptionRegistry.isDefaultSystemConfigurableProvidersLoaded()){
- defaults.add(new SoaplabServiceProviderConfig(
- "http://wsembnet.vital-it.ch/soaplab2-axis/services/"));
- } // else return an empty list
-
- return defaults;
- }
-
- public Icon getIcon() {
- return SoaplabActivityIcon.getSoaplabIcon();
- }
-
- public String getName() {
- return SOAPLAB_SERVICE;
- }
-
- @SuppressWarnings("unchecked")
- protected boolean findSoaplabDetails(
- List<SoaplabServiceDescription> descriptions,
- FindServiceDescriptionsCallBack callBack) {
- Date lastUpdate = new Date();
- // We'll fetch more details and update the descriptions in the
- // background
- List<SoaplabServiceDescription> updatedDescriptions = new ArrayList<SoaplabServiceDescription>();
- for (SoaplabServiceDescription serviceDescription : descriptions) {
- try {
- Date now = new Date();
- if (now.getTime() - lastUpdate.getTime() > DESCRIPTION_UPDATE_INTERVAL_MS) {
- if (!updatedDescriptions.isEmpty()) {
- callBack.partialResults(updatedDescriptions);
- updatedDescriptions = new ArrayList<SoaplabServiceDescription>();
- }
- lastUpdate = now;
- }
- Thread.sleep(DELAY_MS);
- URI soaplabEndpoint = serviceProviderConfig.getEndpoint();
- Map info = (Map) Soap.callWebService(soaplabEndpoint
- .toASCIIString()
- + "/" + serviceDescription.getOperation(),
- "getAnalysisType"); // Get the description element from
- // the map
- String description = (String) info.get("description");
- if (description != null) {
- serviceDescription.setDescription(description);
- }
- updatedDescriptions.add(serviceDescription);
- String type = (String) info.get("type");
- if (type != null) {
- serviceDescription.setTypes(Arrays.asList(type.split(",")));
- }
- } catch (ClassCastException e) {
- logger.warn("Can't read descriptions for soaplab service "
- + serviceDescription, e);
- callBack.warning("Can't read descriptions for soaplab service "
- + serviceDescription.getOperation());
- } catch (ServiceException e) {
- logger.warn("Can't read descriptions for soaplab service "
- + serviceDescription, e);
- callBack.warning("Can't read descriptions for soaplab service "
- + serviceDescription.getOperation());
- } catch (RemoteException e) {
- logger.warn("Can't read descriptions for soaplab service "
- + serviceDescription, e);
- callBack.warning("Can't read descriptions for soaplab service "
- + serviceDescription.getOperation());
- } catch (InterruptedException ex) {
- callBack.fail("Thread was interrupted", ex);
- return false;
- }
- }
- if (!updatedDescriptions.isEmpty()) {
- callBack.partialResults(updatedDescriptions);
- }
- return true;
- }
-
- protected List<SoaplabServiceDescription> findSoaplabServices(
- FindServiceDescriptionsCallBack callBack) {
- List<SoaplabServiceDescription> descriptions = new ArrayList<SoaplabServiceDescription>();
- URI soaplabEndpoint = serviceProviderConfig.getEndpoint();
- callBack.status("Connecting to Soaplab:" + soaplabEndpoint);
- List<SoaplabCategory> categories;
- try {
- categories = SoaplabScavengerAgent.load(soaplabEndpoint
- .toASCIIString());
- } catch (MissingSoaplabException ex) {
- String message = "There was an error with the soaplab: "
- + soaplabEndpoint;
- callBack.fail(message, ex);
- return null;
- }
- for (SoaplabCategory cat : categories) {
- for (String service : cat.getServices()) {
- SoaplabServiceDescription item = new SoaplabServiceDescription();
- item.setCategory(cat.getCategory());
- item.setOperation(service);
- item.setEndpoint(soaplabEndpoint);
- descriptions.add(item);
- }
- }
- return descriptions;
- }
-
- @Override
- protected List<? extends Object> getIdentifyingData() {
- List<String> result;
- result = Arrays.asList(getConfiguration().getEndpoint().toString());
- return result;
- }
-
- public String getId() {
- return providerId.toString();
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProviderConfig.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProviderConfig.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProviderConfig.java
deleted file mode 100644
index d1e86da..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProviderConfig.java
+++ /dev/null
@@ -1,38 +0,0 @@
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
-import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
-
-public class SoaplabServiceProviderConfig extends PropertyAnnotated {
-
- private URI endpoint;
-
- public SoaplabServiceProviderConfig() {
- }
-
- public SoaplabServiceProviderConfig(String endpointURI) {
- this.setEndpoint(URI.create(endpointURI.trim()));
- }
-
- @PropertyAnnotation(displayName = "Soaplab location", preferred = true)
- public URI getEndpoint() {
- return endpoint;
- }
-
- public String toString() {
- return getEndpoint().toString();
- }
-
- public void setEndpoint(URI endpoint) {
- String uriString = endpoint.toString();
- if (!uriString.endsWith("/")) {
- uriString = uriString + "/";
- this.endpoint = URI.create(uriString);
- } else {
- this.endpoint = endpoint;
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
deleted file mode 100644
index de51f23..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
+++ /dev/null
@@ -1,156 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.views;
-
-import java.awt.Frame;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.net.URL;
-
-import javax.swing.Action;
-import javax.xml.namespace.QName;
-import javax.xml.transform.Templates;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
-
-import net.sf.taverna.t2.activities.soaplab.actions.SoaplabActivityConfigurationAction;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.log4j.Logger;
-
-import uk.org.taverna.scufl2.api.activity.Activity;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-public class SoaplabActivityContextualView extends HTMLBasedActivityContextualView {
-
- private static Logger logger = Logger.getLogger(SoaplabActivityContextualView.class);
-
- private static final long serialVersionUID = -6470801873448104509L;
-
- private final EditManager editManager;
-
- private final FileManager fileManager;
-
- private final ActivityIconManager activityIconManager;
-
- private final ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public SoaplabActivityContextualView(Activity activity, EditManager editManager,
- FileManager fileManager, ActivityIconManager activityIconManager,
- ColourManager colourManager, ServiceDescriptionRegistry serviceDescriptionRegistry) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- @Override
- public String getViewTitle() {
- return "Soaplab service";
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- Configuration configuration = getConfigBean();
- JsonNode json = configuration.getJson();
- String html = "<tr><td>Endpoint</td><td>" + json.get("endpoint").textValue() + "</td></tr>";
- html += "<tr><td>Polling interval</td><td>" + json.get("pollingInterval").asText()
- + "</td></tr>";
- html += "<tr><td>Polling backoff</td><td>" + json.get("pollingBackoff").asText()
- + "</td></tr>";
- html += "<tr><td>Polling interval max</td><td>" + json.get("pollingIntervalMax").asText()
- + "</td></tr>";
- // html += "<tr><td>SOAPLAB Metadata</td><td>" + getMetadata()
- // + "</td></tr>";
- return html;
- }
-
- @Override
- public Action getConfigureAction(Frame owner) {
- return new SoaplabActivityConfigurationAction(getActivity(), owner, editManager,
- fileManager, activityIconManager, serviceDescriptionRegistry);
- }
-
- private String getMetadata() {
- try {
- Configuration configuration = getConfigBean();
- JsonNode json = configuration.getJson();
- String endpoint = json.get("endpoint").textValue();
- Call call = (Call) new Service().createCall();
- call.setTimeout(new Integer(0));
- call.setTargetEndpointAddress(endpoint);
- call.setOperationName(new QName("describe"));
- String metadata = (String) call.invoke(new Object[0]);
- logger.info(metadata);
- // Old impl, returns a tree of the XML
- // ColXMLTree tree = new ColXMLTree(metadata);
- URL sheetURL = SoaplabActivityContextualView.class
- .getResource("/analysis_metadata_2_html.xsl");
- TransformerFactory transformerFactory = TransformerFactory.newInstance();
- logger.info(sheetURL.toString());
- Templates stylesheet = transformerFactory.newTemplates(new StreamSource(sheetURL
- .openStream()));
- Transformer transformer = stylesheet.newTransformer();
- StreamSource inputStream = new StreamSource(new ByteArrayInputStream(
- metadata.getBytes()));
- ByteArrayOutputStream transformedStream = new ByteArrayOutputStream();
- StreamResult result = new StreamResult(transformedStream);
- transformer.transform(inputStream, result);
- transformedStream.flush();
- transformedStream.close();
- // String summaryText = "<html><head>"
- // + WorkflowSummaryAsHTML.STYLE_NOBG + "</head>"
- // + transformedStream.toString() + "</html>";
- // JEditorPane metadataPane = new ColJEditorPane("text/html",
- // summaryText);
- // metadataPane.setText(transformedStream.toString());
- // // logger.info(transformedStream.toString());
- // JScrollPane jsp = new JScrollPane(metadataPane,
- // JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
- // JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
- // jsp.setPreferredSize(new Dimension(0, 0));
- // jsp.getVerticalScrollBar().setValue(0);
- return transformedStream.toString();
- } catch (Exception ex) {
- return "<font color=\"red\">Error</font><p>An exception occured while trying to fetch Soaplab metadata from the server. The error was :<pre>"
- + ex.getMessage() + "</pre>";
-
- }
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
deleted file mode 100644
index 23e94d8..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.views;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class SoaplabActivityViewFactory implements ContextualViewFactory<Activity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public boolean canHandle(Object object) {
- return object instanceof Activity && ((Activity) object).getType().equals(SoaplabServiceDescription.ACTIVITY_TYPE);
- }
-
- public List<ContextualView> getViews(Activity activity) {
- return Arrays.asList(new ContextualView[] { new SoaplabActivityContextualView(activity,
- editManager, fileManager, activityIconManager, colourManager, serviceDescriptionRegistry) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
deleted file mode 100644
index fb73ade..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
deleted file mode 100644
index 1eeb850..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.menu.ConfigureSoaplabActivityMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
deleted file mode 100644
index 0bb5227..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
deleted file mode 100644
index ea7da0b..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.views.SoaplabActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/resources/META-INF/spring/soaplab-activity-ui-context-osgi.xml
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diff --git a/src/main/resources/META-INF/spring/soaplab-activity-ui-context-osgi.xml b/src/main/resources/META-INF/spring/soaplab-activity-ui-context-osgi.xml
deleted file mode 100644
index f7e486e..0000000
--- a/src/main/resources/META-INF/spring/soaplab-activity-ui-context-osgi.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="SoaplabActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="SoaplabServiceProvider">
- <interfaces>
- <beans:value>net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider</beans:value>
- <beans:value>net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider</beans:value>
- </interfaces>
- </service>
-
- <service ref="ConfigureSoaplabActivityMenuAction" auto-export="interfaces" />
-
- <service ref="SoaplabActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
-
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/resources/META-INF/spring/soaplab-activity-ui-context.xml
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diff --git a/src/main/resources/META-INF/spring/soaplab-activity-ui-context.xml b/src/main/resources/META-INF/spring/soaplab-activity-ui-context.xml
deleted file mode 100644
index 7f99ff2..0000000
--- a/src/main/resources/META-INF/spring/soaplab-activity-ui-context.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="SoaplabActivityIcon" class="net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabActivityIcon" />
-
- <bean id="SoaplabServiceProvider" class="net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider">
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="ConfigureSoaplabActivityMenuAction" class="net.sf.taverna.t2.activities.soaplab.menu.ConfigureSoaplabActivityMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="SoaplabActivityViewFactory" class="net.sf.taverna.t2.activities.soaplab.views.SoaplabActivityViewFactory" >
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/resources/analysis_metadata_2_html.xsl
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diff --git a/src/main/resources/analysis_metadata_2_html.xsl b/src/main/resources/analysis_metadata_2_html.xsl
deleted file mode 100644
index 5095e5c..0000000
--- a/src/main/resources/analysis_metadata_2_html.xsl
+++ /dev/null
@@ -1,96 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-
-<!-- ===================================================================== -->
-<!-- Converting analysis metadata returned by Soaplab Web Services to HTML -->
-<!-- (http://www.ebi.ac.uk/soaplab/) -->
-<!-- Author: Martin Senger (senger@ebi.ac.uk) -->
-<!-- ===================================================================== -->
-
-<!-- $Id: analysis_metadata_2_html.xsl,v 1.1 2008/07/14 15:27:42 iandunlop Exp $ -->
-
-<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
- version="1.0">
- <xsl:output method="html"/>
-
- <!-- the main document body -->
- <xsl:template match="/">
- <body>
- <xsl:apply-templates/>
- </body>
- </xsl:template>
-
- <!-- analysis -->
- <xsl:template match="/DsLSRAnalysis/analysis">
-
- <!-- analysis name -->
- <table border="0" cellpadding="2" cellspacing="3" width="98%" align="center"><tr><th bgcolor="#eeeedd">
- <font size="+1"><xsl:value-of select="@name"/></font>
- </th></tr></table>
-
- <!-- analysis metadata -->
- <table border="0" cellspacing="1" cellpadding="1" width="99%" align="center"><tr>
- <td>
- <table border="0" cellspacing="2">
- <xsl:apply-templates select="description" mode="as-row"/>
- <xsl:apply-templates select="analysis_extension/app_info/@*[local-name != 'help_URL']" mode="as-row"/>
- <xsl:apply-templates select="@*[local-name() != 'name']" mode="as-row"/>
- <tr><td>Help URL</td><td><a href="{analysis_extension/app_info/@help_URL}"><xsl:value-of select="analysis_extension/app_info/@help_URL"/></a></td></tr>
- </table>
- </td></tr></table>
-
- <!-- inputs/outputs metadata -->
- <table border="0" width="98%" cellpadding="2" cellspacing="1" align="center">
- <tr><td colspan="2" bgcolor="#eeeedd"> <b>Outputs</b> </td></tr>
- <xsl:apply-templates select="output"/>
- <tr><td colspan="2" bgcolor="#eeeedd"> <b>Inputs</b> </td></tr>
- <xsl:apply-templates select="input"/>
- </table>
-
- </xsl:template>
-
- <!-- metadata about one input or output -->
- <xsl:template match="input|output">
- <xsl:variable name="param_name" select="@name"/>
- <tr bgcolor="#eae9c2">
- <td valign="top"><b><xsl:value-of select="@name"/></b></td>
- <td><table border="0" cellspacing="1" cellpadding="1" bgcolor="white" width="100%">
- <xsl:apply-templates select="@*[local-name() != 'name']" mode="as-row"/>
- <xsl:apply-templates select="allowed" mode="as-row"/>
- <xsl:apply-templates select="../analysis_extension/parameter/base[@name =$param_name]/*" mode="as-row"/>
- <xsl:apply-templates select="../analysis_extension/parameter/base[concat(@name,'_url') =$param_name]/*" mode="as-row"/>
- <xsl:apply-templates select="../analysis_extension/parameter/base[concat(@name,'_direct_data')=$param_name]/*" mode="as-row"/>
- <xsl:apply-templates select="../analysis_extension/parameter/base[concat(@name,'_usa') =$param_name]/*" mode="as-row"/>
- </table></td>
- </tr>
- </xsl:template>
-
- <!-- attributes and elements expressed as a (bold)name and value -->
- <xsl:template match="@*[local-name() != 'help_URL']|description|default|prompt|help" mode="as-row">
- <tr>
- <td valign="top" width="80"><em><xsl:value-of select="local-name()"/></em></td>
- <td><xsl:value-of select="."/></td>
- </tr>
- </xsl:template>
-
- <!-- more-values elements -->
- <xsl:template match="allowed" mode="as-row">
-
- <xsl:if test="position() = 1">
- <xsl:text disable-output-escaping = "yes"><tr></xsl:text>
- <td valign="top" width="80"><em><xsl:value-of select="local-name()"/></em></td>
- <xsl:text disable-output-escaping = "yes"><td></xsl:text>
- </xsl:if>
-
- <xsl:value-of select="."/>
- <xsl:if test="position() != last()">
- <xsl:text>, </xsl:text>
- </xsl:if>
-
- <xsl:if test="position() = last()">
- <xsl:text disable-output-escaping = "yes"></td></xsl:text>
- <xsl:text disable-output-escaping = "yes"></tr></xsl:text>
- </xsl:if>
-
- </xsl:template>
-
-</xsl:stylesheet>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/main/resources/soaplab.png
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diff --git a/src/main/resources/soaplab.png b/src/main/resources/soaplab.png
deleted file mode 100644
index b86d848..0000000
Binary files a/src/main/resources/soaplab.png and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
----------------------------------------------------------------------
diff --git a/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java b/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
deleted file mode 100644
index c4d683d..0000000
--- a/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.views;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.activities.soaplab.actions.SoaplabActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class TestSoaplabActivityContextualView {
-
- Activity a;
-
- @Before
- public void setup() throws Exception {
- a=new Activity();
- }
-
- @Test
- @Ignore("Integration test")
- public void testConfigureAction() throws Exception {
- ContextualView view = new SoaplabActivityContextualView(a, null, null, null, null, null);
- assertNotNull("the action should not be null",view.getConfigureAction(null));
- assertTrue("The action should be a SoaplabAcitivyConfigurationAction",view.getConfigureAction(null) instanceof SoaplabActivityConfigurationAction);
- }
-
- private void run() throws Exception
- {
- setup();
- ContextualView view = new SoaplabActivityContextualView(a, null, null, null, null, null);
- view.setVisible(true);
- }
-
- public static void main(String[] args) throws Exception {
- new TestSoaplabActivityContextualView().run();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/taverna-soaplab-activity-ui/pom.xml
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diff --git a/taverna-soaplab-activity-ui/pom.xml b/taverna-soaplab-activity-ui/pom.xml
new file mode 100644
index 0000000..737a13d
--- /dev/null
+++ b/taverna-soaplab-activity-ui/pom.xml
@@ -0,0 +1,103 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>soaplab-activity-ui</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>Taverna 2 Soaplab Activity UI</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>soaplab-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-tools</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>edits-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>file-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>menu-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.axis</groupId>
+ <artifactId>com.springsource.org.apache.axis</artifactId>
+ <version>${axis.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.xml.rpc</groupId>
+ <artifactId>com.springsource.javax.xml.rpc</artifactId>
+ <version>${xml.rpc.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+ <scm>
+ <connection>scm:git:https://github.com/taverna/taverna-soaplab-activity-ui.git</connection>
+ <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-soaplab-activity-ui.git</developerConnection>
+ <url>https://github.com/taverna/taverna-soaplab-activity-ui/</url>
+ <tag>HEAD</tag>
+ </scm>
+
+</project>
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/418e332b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
new file mode 100644
index 0000000..43b87f1
--- /dev/null
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
@@ -0,0 +1,68 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.soaplab.actions;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+public class SoaplabActivityConfigurationAction extends ActivityConfigurationAction {
+
+ private static final long serialVersionUID = 5076721332542691094L;
+ private final Frame owner;
+ public static final String CONFIGURE_SOAPLAB_ACTIVITY = "Configure Soaplab";
+ private final EditManager editManager;
+ private final FileManager fileManager;
+
+ public SoaplabActivityConfigurationAction(Activity activity, Frame owner,
+ EditManager editManager, FileManager fileManager,
+ ActivityIconManager activityIconManager, ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ super(activity, activityIconManager, serviceDescriptionRegistry);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ putValue(Action.NAME, CONFIGURE_SOAPLAB_ACTIVITY);
+ this.owner = owner;
+ }
+
+ public void actionPerformed(ActionEvent action) {
+ ActivityConfigurationDialog currentDialog = ActivityConfigurationAction.getDialog(getActivity());
+ if (currentDialog != null) {
+ currentDialog.toFront();
+ return;
+ }
+
+ final SoaplabConfigurationPanel panel = new SoaplabConfigurationPanel(getActivity());
+ final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(
+ getActivity(), panel, editManager);
+
+ ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
+ }
+
+}