http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java deleted file mode 100644 index 43bc61f..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java +++ /dev/null @@ -1,220 +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 - * USA. - * - */ -package net.sf.taverna.t2.activities.biomoby.edits; - -import java.util.ArrayList; -import java.util.List; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivity; -import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean; -import net.sf.taverna.t2.workflowmodel.CompoundEdit; -import net.sf.taverna.t2.workflowmodel.Dataflow; -import net.sf.taverna.t2.workflowmodel.Edit; -import net.sf.taverna.t2.workflowmodel.EditException; -import net.sf.taverna.t2.workflowmodel.Edits; -import net.sf.taverna.t2.workflowmodel.EventForwardingOutputPort; -import net.sf.taverna.t2.workflowmodel.EventHandlingInputPort; -import net.sf.taverna.t2.workflowmodel.InputPort; -import net.sf.taverna.t2.workflowmodel.OutputPort; -import net.sf.taverna.t2.workflowmodel.Processor; -import net.sf.taverna.t2.workflowmodel.ProcessorInputPort; -import net.sf.taverna.t2.workflowmodel.ProcessorOutputPort; -import net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit; -import net.sf.taverna.t2.workflowmodel.impl.DataflowImpl; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; -import net.sf.taverna.t2.workflowmodel.utils.Tools; - -/** - * @author Stuart Owen - * - */ -public class AddMobyParseDatatypeEdit extends AbstractDataflowEdit { - - private final BiomobyActivity activity; - private final String objectName; - private final boolean isCollection; - private final String potentialCollectionString; - - private Edit<?> compoundEdit = null; - private Edit<?> linkEdit = null; - - private Edits edits; - - /** - * @param dataflow - */ - public AddMobyParseDatatypeEdit(Dataflow dataflow, - BiomobyActivity activity, String objectName, boolean isCollection, - String potentialCollectionString, Edits edits) { - super(dataflow); - this.activity = activity; - this.objectName = objectName; - this.isCollection = isCollection; - this.potentialCollectionString = potentialCollectionString; - this.edits = edits; - } - - /* - * (non-Javadoc) - * - * @see - * net.sf.taverna.t2.workflowmodel.impl.AbstractEdit#doEditAction(java.lang - * .Object) - */ - @Override - protected void doEditAction(DataflowImpl dataflow) throws EditException { - - List<Edit<?>> editList = new ArrayList<Edit<?>>(); - - String defaultName = objectName; - if (defaultName.indexOf("(") > 0) - defaultName = defaultName.substring(0, defaultName.indexOf("(")); - - String name = Tools - .uniqueProcessorName("Parse Moby Data(" + defaultName + ")", - dataflow); - - String articlename = ""; - if (isCollection) { - articlename = potentialCollectionString.substring( - potentialCollectionString.indexOf("('") + 2, - potentialCollectionString.lastIndexOf("'")); - } else { - articlename = objectName.substring(objectName.indexOf("'") + 1, - objectName.lastIndexOf("'")); - } - - MobyParseDatatypeActivityConfigurationBean bean = new MobyParseDatatypeActivityConfigurationBean(); - bean.setArticleNameUsedByService(articlename); - bean.setRegistryEndpoint(activity.getConfiguration().getMobyEndpoint()); - bean.setDatatypeName(defaultName); - MobyParseDatatypeActivity mobyDatatypeActivity = new MobyParseDatatypeActivity(); - - editList - .add(edits.getConfigureActivityEdit(mobyDatatypeActivity, bean)); - - net.sf.taverna.t2.workflowmodel.Processor sinkProcessor = edits - .createProcessor(name); - - editList.add(edits.getDefaultDispatchStackEdit(sinkProcessor)); - - Edit<?> addActivityToProcessorEdit = edits.getAddActivityEdit( - sinkProcessor, mobyDatatypeActivity); - editList.add(addActivityToProcessorEdit); - - editList.add(edits.getAddProcessorEdit(dataflow, sinkProcessor)); - - compoundEdit = new CompoundEdit(editList); - compoundEdit.doEdit(); - - Processor sourceProcessor = Tools.getProcessorsWithActivity(dataflow, - activity).iterator().next(); - - List<Edit<?>> linkEditList = new ArrayList<Edit<?>>(); - - String inputName = mobyDatatypeActivity.getInputPorts().iterator() - .next().getName(); - EventHandlingInputPort sinkPort = getSinkPort(sinkProcessor, - mobyDatatypeActivity, inputName, linkEditList); - - - String outputPortName; - if (isCollection) { - outputPortName = defaultName + "(Collection - '" - + (articlename.equals("") ? "MobyCollection" : articlename) - + "' As Simples)"; - } - else { - outputPortName = defaultName +"(" + articlename + ")"; - } - EventForwardingOutputPort sourcePort = getSourcePort(sourceProcessor, - activity, outputPortName, linkEditList); - linkEditList.add(Tools.getCreateAndConnectDatalinkEdit(dataflow, - sourcePort, sinkPort, edits)); - linkEdit = new CompoundEdit(linkEditList); - linkEdit.doEdit(); - - } - - /* - * (non-Javadoc) - * - * @see - * net.sf.taverna.t2.workflowmodel.impl.AbstractEdit#undoEditAction(java - * .lang.Object) - */ - @Override - protected void undoEditAction(DataflowImpl subjectImpl) { - if (linkEdit != null && linkEdit.isApplied()) - linkEdit.undo(); - if (compoundEdit != null && compoundEdit.isApplied()) - compoundEdit.undo(); - } - - private EventHandlingInputPort getSinkPort( - net.sf.taverna.t2.workflowmodel.Processor processor, - Activity<?> activity, String portName, List<Edit<?>> editList) { - InputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools - .getActivityInputPort(activity, portName); - // check if processor port exists - EventHandlingInputPort input = net.sf.taverna.t2.workflowmodel.utils.Tools - .getProcessorInputPort(processor, activity, activityPort); - if (input == null) { - // port doesn't exist so create a processor port and map it - ProcessorInputPort processorInputPort = edits - .createProcessorInputPort(processor, - activityPort.getName(), activityPort.getDepth()); - editList.add(edits.getAddProcessorInputPortEdit(processor, - processorInputPort)); - editList.add(edits.getAddActivityInputPortMappingEdit(activity, - activityPort.getName(), activityPort.getName())); - input = processorInputPort; - } - return input; - } - - private EventForwardingOutputPort getSourcePort( - net.sf.taverna.t2.workflowmodel.Processor processor, - Activity<?> activity, String portName, List<Edit<?>> editList) { - OutputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools - .getActivityOutputPort(activity, portName); - // check if processor port exists - EventForwardingOutputPort output = net.sf.taverna.t2.workflowmodel.utils.Tools - .getProcessorOutputPort(processor, activity, activityPort); - if (output == null) { - // port doesn't exist so create a processor port and map it - ProcessorOutputPort processorOutputPort = edits - .createProcessorOutputPort(processor, activityPort - .getName(), activityPort.getDepth(), activityPort - .getGranularDepth()); - editList.add(edits.getAddProcessorOutputPortEdit(processor, - processorOutputPort)); - editList.add(edits.getAddActivityOutputPortMappingEdit(activity, - activityPort.getName(), activityPort.getName())); - output = processorOutputPort; - } - return output; - } - -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java deleted file mode 100644 index fea1860..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java +++ /dev/null @@ -1,216 +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 - * USA. - * - */ -package net.sf.taverna.t2.activities.biomoby.edits; - -import java.util.ArrayList; -import java.util.List; - -import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean; -import net.sf.taverna.t2.workflowmodel.CompoundEdit; -import net.sf.taverna.t2.workflowmodel.Dataflow; -import net.sf.taverna.t2.workflowmodel.Edit; -import net.sf.taverna.t2.workflowmodel.EditException; -import net.sf.taverna.t2.workflowmodel.Edits; -import net.sf.taverna.t2.workflowmodel.EventForwardingOutputPort; -import net.sf.taverna.t2.workflowmodel.EventHandlingInputPort; -import net.sf.taverna.t2.workflowmodel.InputPort; -import net.sf.taverna.t2.workflowmodel.OutputPort; -import net.sf.taverna.t2.workflowmodel.Processor; -import net.sf.taverna.t2.workflowmodel.ProcessorInputPort; -import net.sf.taverna.t2.workflowmodel.ProcessorOutputPort; -import net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit; -import net.sf.taverna.t2.workflowmodel.impl.DataflowImpl; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; -import net.sf.taverna.t2.workflowmodel.utils.Tools; - -import org.apache.log4j.Logger; - -/** - * @author Stuart Owen - * - */ -public class AddUpstreamObjectEdit extends AbstractDataflowEdit { - - private static Logger logger = Logger.getLogger(AddUpstreamObjectEdit.class); - - private final Processor sinkProcessor; - private final BiomobyObjectActivity activity; - private Edits edits; - - private List<Edit<?>> subEdits = new ArrayList<Edit<?>>(); - - /** - * @param dataflow - */ - public AddUpstreamObjectEdit(Dataflow dataflow, Processor sinkProcessor, - BiomobyObjectActivity activity, Edits edits) { - super(dataflow); - this.sinkProcessor = sinkProcessor; - this.activity = activity; - this.edits = edits; - } - - /* - * (non-Javadoc) - * - * @see - * net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit#doEditAction - * (net.sf.taverna.t2.workflowmodel.impl.DataflowImpl) - */ - @Override - protected void doEditAction(DataflowImpl dataflow) throws EditException { - subEdits.clear(); - - for (InputPort inputPort : activity.getInputPorts()) { - // ignore article name, id, namespace, value - if (inputPort.getName().equals("namespace") - || inputPort.getName().equals("id") - || inputPort.getName().equals("article name") - || inputPort.getName().equals("value")) { - continue; - } - List<Edit<?>> editList = new ArrayList<Edit<?>>(); - String defaultName = inputPort.getName().split("\\(")[0]; - - String name = Tools - .uniqueProcessorName(inputPort.getName(), dataflow); - - BiomobyObjectActivityConfigurationBean configBean = new BiomobyObjectActivityConfigurationBean(); - configBean.setMobyEndpoint(activity.getConfiguration() - .getMobyEndpoint()); - configBean.setAuthorityName(""); - configBean.setServiceName(defaultName); - - net.sf.taverna.t2.workflowmodel.Processor sourceProcessor = edits - .createProcessor(name); - BiomobyObjectActivity boActivity = new BiomobyObjectActivity(); - Edit<?> configureActivityEdit = edits.getConfigureActivityEdit( - boActivity, configBean); - editList.add(configureActivityEdit); - - editList.add(edits.getDefaultDispatchStackEdit(sourceProcessor)); - - Edit<?> addActivityToProcessorEdit = edits.getAddActivityEdit( - sourceProcessor, boActivity); - editList.add(addActivityToProcessorEdit); - - - - editList.add(edits.getAddProcessorEdit(dataflow, sourceProcessor)); - - CompoundEdit compoundEdit = new CompoundEdit(editList); - subEdits.add(compoundEdit); - compoundEdit.doEdit(); - - - List<Edit<?>> linkEditList = new ArrayList<Edit<?>>(); - - EventForwardingOutputPort sourcePort = getSourcePort( - sourceProcessor, boActivity, "mobyData", linkEditList); - EventHandlingInputPort sinkPort = getSinkPort(sinkProcessor, activity, inputPort.getName(), linkEditList); - linkEditList.add(Tools.getCreateAndConnectDatalinkEdit(dataflow, - sourcePort, sinkPort, edits)); - CompoundEdit linkEdit = new CompoundEdit(linkEditList); - subEdits.add(linkEdit); - linkEdit.doEdit(); - - if (!(defaultName.equalsIgnoreCase("Object") - || name.equalsIgnoreCase("String") - || name.equalsIgnoreCase("Integer") || name - .equalsIgnoreCase("DateTime"))) { - Edit upstreamObjectEdit = new AddUpstreamObjectEdit(dataflow, - sourceProcessor, boActivity, edits); - subEdits.add(upstreamObjectEdit); - upstreamObjectEdit.doEdit(); - } - } - - } - - /* - * (non-Javadoc) - * - * @see - * net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit#undoEditAction - * (net.sf.taverna.t2.workflowmodel.impl.DataflowImpl) - */ - @Override - protected void undoEditAction(DataflowImpl dataflow) { - if (subEdits != null && subEdits.size() > 0) { - for (int i = subEdits.size() - 1; i >= 0; i--) { - Edit<?> edit = subEdits.get(i); - if (edit.isApplied()) - edit.undo(); - } - } - - - } - - private EventHandlingInputPort getSinkPort( - net.sf.taverna.t2.workflowmodel.Processor processor, - Activity<?> activity, String portName, List<Edit<?>> editList) { - InputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools - .getActivityInputPort(activity, portName); - // check if processor port exists - EventHandlingInputPort input = net.sf.taverna.t2.workflowmodel.utils.Tools - .getProcessorInputPort(processor, activity, activityPort); - if (input == null) { - // port doesn't exist so create a processor port and map it - ProcessorInputPort processorInputPort = edits - .createProcessorInputPort(processor, - activityPort.getName(), activityPort.getDepth()); - editList.add(edits.getAddProcessorInputPortEdit(processor, - processorInputPort)); - editList.add(edits.getAddActivityInputPortMappingEdit(activity, - activityPort.getName(), activityPort.getName())); - input = processorInputPort; - } - return input; - } - - private EventForwardingOutputPort getSourcePort( - net.sf.taverna.t2.workflowmodel.Processor processor, - Activity<?> activity, String portName, List<Edit<?>> editList) { - OutputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools - .getActivityOutputPort(activity, portName); - // check if processor port exists - EventForwardingOutputPort output = net.sf.taverna.t2.workflowmodel.utils.Tools - .getProcessorOutputPort(processor, activity, activityPort); - if (output == null) { - // port doesn't exist so create a processor port and map it - ProcessorOutputPort processorOutputPort = edits - .createProcessorOutputPort(processor, activityPort - .getName(), activityPort.getDepth(), activityPort - .getGranularDepth()); - editList.add(edits.getAddProcessorOutputPortEdit(processor, - processorOutputPort)); - editList.add(edits.getAddActivityOutputPortMappingEdit(activity, - activityPort.getName(), activityPort.getName())); - output = processorOutputPort; - } - return output; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityDetailsMenuAction.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityDetailsMenuAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityDetailsMenuAction.java deleted file mode 100644 index cee5420..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityDetailsMenuAction.java +++ /dev/null @@ -1,40 +0,0 @@ -package net.sf.taverna.t2.activities.biomoby.menu; - -import javax.swing.Action; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.actions.MobyServiceDetailsAction; -import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workflowmodel.Edits; - -public class BiomobyActivityDetailsMenuAction extends - AbstractConfigureActivityMenuAction<BiomobyActivity> { - - private static final String CONFIGURE_BIOMOBY_DETAILS = "Browse Biomoby service details"; - private EditManager editManager; - private FileManager fileManager; - - public BiomobyActivityDetailsMenuAction() { - super(BiomobyActivity.class); - } - - @Override - protected Action createAction() { - MobyServiceDetailsAction configAction = new MobyServiceDetailsAction( - findActivity(), getParentFrame(), editManager, fileManager); - configAction.putValue(Action.NAME, CONFIGURE_BIOMOBY_DETAILS); - addMenuDots(configAction); - return configAction; - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setFileManager(FileManager fileManager) { - this.fileManager = fileManager; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityParserMenuAction.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityParserMenuAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityParserMenuAction.java deleted file mode 100644 index b760bbc..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityParserMenuAction.java +++ /dev/null @@ -1,41 +0,0 @@ -package net.sf.taverna.t2.activities.biomoby.menu; - -import javax.swing.Action; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.actions.MobyParserAction; -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 BiomobyActivityParserMenuAction extends - AbstractConfigureActivityMenuAction<BiomobyActivity> { - - private static final String ADD_BIOMOBY_PARSER = "Add Biomoby parser"; - - private EditManager editManager; - - private FileManager fileManager; - - public BiomobyActivityParserMenuAction() { - super(BiomobyActivity.class); - } - - @Override - protected Action createAction() { - MobyParserAction configAction = new MobyParserAction( - findActivity(), getParentFrame(), editManager, fileManager); - configAction.putValue(Action.NAME, ADD_BIOMOBY_PARSER); - addMenuDots(configAction); - return configAction; - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setFileManager(FileManager fileManager) { - this.fileManager = fileManager; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/ConfigureBiomobyMenuAction.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/ConfigureBiomobyMenuAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/ConfigureBiomobyMenuAction.java deleted file mode 100644 index b86df2a..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/ConfigureBiomobyMenuAction.java +++ /dev/null @@ -1,52 +0,0 @@ -package net.sf.taverna.t2.activities.biomoby.menu; - -import javax.swing.Action; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.actions.BiomobyActivityConfigurationAction; -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 ConfigureBiomobyMenuAction extends - AbstractConfigureActivityMenuAction<BiomobyActivity> { - - private EditManager editManager; - private FileManager fileManager; - private ActivityIconManager activityIconManager; - - public ConfigureBiomobyMenuAction() { - super(BiomobyActivity.class); - } - - @Override - protected Action createAction() { - BiomobyActivity a = findActivity(); - Action result = null; - result = new BiomobyActivityConfigurationAction(a, getParentFrame(), editManager, - fileManager, activityIconManager); - result.putValue(Action.NAME, "Configure"); - addMenuDots(result); - return result; - } - - public boolean isEnabled() { - BiomobyActivity activity = findActivity(); - return (super.isEnabled() && (activity.getMobyService() != null) && activity - .containsSecondaries()); - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setFileManager(FileManager fileManager) { - this.fileManager = fileManager; - } - - public void setActivityIconManager(ActivityIconManager activityIconManager) { - this.activityIconManager = activityIconManager; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java deleted file mode 100644 index 2c28c32..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java +++ /dev/null @@ -1,36 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby.query; - -import javax.swing.Icon; -import javax.swing.ImageIcon; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; - -/** - * - * @author Alex Nenadic - * - */ -public class BiomobyActivityIcon implements ActivityIconSPI{ - - public int canProvideIconScore(Activity<?> activity) { - if (activity.getClass().getName().equals(BiomobyActivity.class.getName())) - return DEFAULT_ICON + 1; - else - return NO_ICON; - } - - public Icon getIcon(Activity<?> activity) { - return getBiomobyIcon(); - } - - public static Icon getBiomobyIcon() { - return new ImageIcon(BiomobyActivityIcon.class.getResource("/registry.gif")); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java deleted file mode 100644 index a799280..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java +++ /dev/null @@ -1,94 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby.query; - - -public class BiomobyActivityItem /*extends AbstractActivityItem */{ - - String registryUrl; - String serviceName; - String authorityName; - String registryUri; - String category; - String serviceType; - - public String getRegistryUri() { - return registryUri; - } - - public void setRegistryUri(String registryUri) { - this.registryUri = registryUri; - } - - public String getRegistryUrl() { - return registryUrl; - } - - public void setRegistryUrl(String registryUrl) { - this.registryUrl = registryUrl; - } - - public String getServiceName() { - return serviceName; - } - - public void setServiceName(String serviceName) { - this.serviceName = serviceName; - } - - public String getAuthorityName() { - return authorityName; - } - - public void setAuthorityName(String authorityName) { - this.authorityName = authorityName; - } - -// @Override -// public Object getConfigBean() { -// BiomobyActivityConfigurationBean bean = new BiomobyActivityConfigurationBean(); -// bean.setAuthorityName(getAuthorityName()); -// bean.setServiceName(getServiceName()); -// bean.setMobyEndpoint(getRegistryUrl()); -// return bean; -// } -// -// @Override -// public Icon getIcon() { -// return BiomobyActivityIcon.getBiomobyIcon(); -// } -// -// @Override -// public Activity<?> getUnconfiguredActivity() { -// return new BiomobyActivity(); -// } - - public String getType() { - return "Biomoby"; - } - - @Override - public String toString() { - return getServiceName(); - } - - public String getCategory() { - return category; - } - - public void setCategory(String category) { - this.category = category; - } - - public String getServiceType() { - return serviceType; - } - - public void setServiceType(String serviceType) { - this.serviceType = serviceType; - } - - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java deleted file mode 100644 index f4575e4..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java +++ /dev/null @@ -1,32 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby.query; - -import javax.swing.Icon; -import javax.swing.ImageIcon; - -import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity; -import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; - -/** - * - * @author Alex Nenadic - * - */ -public class BiomobyObjectActivityIcon implements ActivityIconSPI{ - - public int canProvideIconScore(Activity<?> activity) { - if (activity.getClass().getName().equals(BiomobyObjectActivity.class.getName())) - return DEFAULT_ICON + 1; - else - return NO_ICON; - } - - public Icon getIcon(Activity<?> activity) { - return new ImageIcon(BiomobyObjectActivityIcon.class.getResource("/biomoby_object.png")); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java deleted file mode 100644 index 1e50d37..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java +++ /dev/null @@ -1,76 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby.query; - - -/** - * - * @author Alex Nenadic - * @author Stuart Owen - * - */ -public class BiomobyObjectActivityItem /*extends AbstractActivityItem*/ { - - String registryUrl; - String serviceName; - String authorityName; - String registryUri; - - public String getRegistryUri() { - return registryUri; - } - - public void setRegistryUri(String registryUri) { - this.registryUri = registryUri; - } - - public String getRegistryUrl() { - return registryUrl; - } - - public void setRegistryUrl(String registryUrl) { - this.registryUrl = registryUrl; - } - - public String getServiceName() { - return serviceName; - } - - public void setServiceName(String serviceName) { - this.serviceName = serviceName; - } - - public String getAuthorityName() { - return authorityName; - } - - public void setAuthorityName(String authorityName) { - this.authorityName = authorityName; - } - -// @Override -// public Object getConfigBean() { -// BiomobyObjectActivityConfigurationBean bean = new BiomobyObjectActivityConfigurationBean(); -// bean.setAuthorityName(getAuthorityName()); -// bean.setServiceName(getServiceName()); -// bean.setMobyEndpoint(getRegistryUrl()); -// return bean; -// } -// -// @Override -// public Icon getIcon() { -// return new ImageIcon(BiomobyObjectActivityItem.class.getResource("/biomoby_object.png")); -// } -// -// @Override -// public Activity<?> getUnconfiguredActivity() { -// return new BiomobyObjectActivity(); -// } - - public String getType() { - return "Biomoby Object"; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java deleted file mode 100644 index e22b78c..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java +++ /dev/null @@ -1,270 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby.query; - -import java.io.File; -import java.io.InputStream; -import java.net.URI; -import java.util.ArrayList; -import java.util.Comparator; -import java.util.List; -import java.util.SortedMap; -import java.util.SortedSet; -import java.util.TreeMap; -import java.util.TreeSet; - -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; - -import net.sf.taverna.raven.appconfig.ApplicationRuntime; -import net.sf.taverna.t2.activities.biomoby.GetOntologyThread; -import net.sf.taverna.t2.activities.biomoby.datatypedescriptions.BiomobyDatatypeDescription; -import net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceDescription; -import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider.FindServiceDescriptionsCallBack; - -import org.apache.log4j.Logger; -import org.biomoby.client.CentralDigestCachedImpl; -import org.biomoby.client.CentralImpl; -import org.biomoby.shared.MobyDataType; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.MobyService; -import org.w3c.dom.Document; - -public class BiomobyQueryHelper { - - private static Logger log = Logger.getLogger(BiomobyQueryHelper.class); - - private String registryNamespace; - private String registryEndpoint; - - private CentralDigestCachedImpl central; - - private String DEFAULT_REGISTRY_ENDPOINT = CentralImpl.DEFAULT_ENDPOINT; - - private String DEFAULT_REGISTRY_NAMESPACE = CentralImpl.DEFAULT_NAMESPACE; - - private String remoteDatatypeRdfUrl = null; - - private String remoteServiceRdfUrl = null; - - private static final String CACHE_NAME = "moby-cache"; - - private ApplicationRuntime applicationRuntime = ApplicationRuntime - .getInstance(); - - public BiomobyQueryHelper(String registryEndpoint, String registryNamespace) - throws MobyException { - try { - if (registryNamespace != null) - this.registryNamespace = registryNamespace; - else - this.registryNamespace = DEFAULT_REGISTRY_NAMESPACE; - if (registryEndpoint != null) - this.registryEndpoint = registryEndpoint; - else - this.registryEndpoint = DEFAULT_REGISTRY_ENDPOINT; - String tavernaHome = null; - if (applicationRuntime.getApplicationHomeDir() != null) { - tavernaHome = applicationRuntime.getApplicationHomeDir() - .getAbsolutePath(); - } - String cacheLoc = tavernaHome; - if (cacheLoc == null || cacheLoc.trim().length() == 0) - cacheLoc = ""; - if (!cacheLoc.endsWith(System.getProperty("file.separator"))) - cacheLoc += File.separator; - - central = new CentralDigestCachedImpl(this.registryEndpoint, - this.registryNamespace, cacheLoc + CACHE_NAME); - - } catch (MobyException e) { - // - log.warn("There was a problem in initializing the caching agent, therefor caching is disabled.", - e); - } - // now we try to speed up the loading of the datatypes ontology - try { - new GetOntologyThread(central.getRegistryEndpoint()).start(); - } catch (Exception e) { - /* don't care if an exception occurs here ... */ - } - // just call this to ensure that the registry is valid - // throws exception if it isnt - central.getResourceRefs(); - } - - /** - * - * @return an ArrayList of BiomobyActivityItem - * @throws MobyException - * if something goes wrong - */ - public synchronized ArrayList<BiomobyActivityItem> getServices() - throws MobyException { - central.updateCache(CentralDigestCachedImpl.CACHE_PART_SERVICES); - MobyService[] services = central.getServices(); - SortedMap<String, SortedSet<MobyService>> map = new TreeMap<String, SortedSet<MobyService>>(); - for (MobyService service : services) { - String authority = service.getAuthority(); - SortedSet<MobyService> set; - if (map.containsKey(authority)) { - set = map.remove(authority); - set.add(service); - map.put(authority, set); - } else { - set = new TreeSet<MobyService>(new Comparator<MobyService>() { - public int compare(MobyService o1, MobyService o2) { - return o1.getName().compareTo(o2.getName()); - } - }); - set.add(service); - map.put(authority, set); - } - } - ArrayList<BiomobyActivityItem> authorityList = new ArrayList<BiomobyActivityItem>(); - for (String authority_name : map.keySet()) { - for (MobyService service : map.get(authority_name)) { - String serviceName = service.getName(); - // if (service.getStatus() != MobyService.UNCHECKED) { - // f.setAlive((service.getStatus() & MobyService.ALIVE) == 2); - // } - BiomobyActivityItem item = makeActivityItem(registryEndpoint, - registryNamespace, authority_name, serviceName); - item.setCategory(service.getCategory()); - item.setServiceType(service.getServiceType() == null ? "Service" - : service.getServiceType().getName()); - authorityList.add(item); - } - } - return authorityList; - - } - - private BiomobyActivityItem makeActivityItem(String url, String uri, - String authorityName, String serviceName) { - BiomobyActivityItem item = new BiomobyActivityItem(); - item.setAuthorityName(authorityName); - item.setServiceName(serviceName); - item.setRegistryUrl(url); - item.setRegistryUri(uri); - return item; - } - - public String getRemoteDatatypeRdfUrl() { - return remoteDatatypeRdfUrl; - } - - public String getRemoteServiceRdfUrl() { - return remoteServiceRdfUrl; - } - - public static Document loadDocument(InputStream input) throws MobyException { - try { - DocumentBuilderFactory dbf = (DocumentBuilderFactory) DOCUMENT_BUILDER_FACTORIES - .get(); - DocumentBuilder db = dbf.newDocumentBuilder(); - return (db.parse(input)); - } catch (Exception e) { - throw new MobyException("Problem with reading XML input: " - + e.toString(), e); - } - } - - public static ThreadLocal<DocumentBuilderFactory> DOCUMENT_BUILDER_FACTORIES = new ThreadLocal<DocumentBuilderFactory>() { - protected synchronized DocumentBuilderFactory initialValue() { - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - dbf.setNamespaceAware(true); - return dbf; - } - }; - - public void findServiceDescriptionsAsync( - FindServiceDescriptionsCallBack callBack) { - try { - central.updateCache(CentralDigestCachedImpl.CACHE_PART_SERVICES); - } catch (MobyException ex) { - callBack.fail("Can't update the Biomoby cache", ex); - return; - } - MobyService[] services; - try { - services = central.getServices(); - } catch (MobyException ex) { - callBack.fail("Can't get BioMoby services", ex); - return; - } - List<BiomobyServiceDescription> serviceDescriptions = new ArrayList<BiomobyServiceDescription>(); - for (MobyService service : services) { - BiomobyServiceDescription serviceDesc = new BiomobyServiceDescription(); - serviceDesc.setEndpoint(URI.create(registryEndpoint)); - serviceDesc.setNamespace(URI.create(registryNamespace)); - serviceDesc.setAuthorityName(service.getAuthority()); - serviceDesc.setServiceName(service.getName()); - serviceDesc.setCategory(service.getCategory()); - serviceDesc.setDescription(service.getDescription()); - String lsid = service.getLSID(); - if (lsid != null && lsid.length() > 0) { - serviceDesc.setLSID(URI.create(lsid)); - } - serviceDesc.setEmailContact(service.getEmailContact()); - serviceDesc.setServiceType(service.getServiceType() == null ? "Service" - : service.getServiceType().getName()); - String signatureURL = service.getSignatureURL(); - if (signatureURL != null && signatureURL.length() > 0) { - serviceDesc.setSignatureURI(URI.create(signatureURL)); - } - serviceDescriptions.add(serviceDesc); - } - callBack.partialResults(serviceDescriptions); - callBack.partialResults(findDatatypeDescriptions()); - callBack.finished(); - } - - public List<BiomobyDatatypeDescription> findDatatypeDescriptions() { - try { - central.updateCache(CentralDigestCachedImpl.CACHE_PART_DATATYPES); - } catch (MobyException ex) { - - return new ArrayList<BiomobyDatatypeDescription>(); - } - MobyDataType[] datatypes; - try { - datatypes = central.getDataTypes(); - } catch (MobyException ex) { - - return new ArrayList<BiomobyDatatypeDescription>(); - } - List<BiomobyDatatypeDescription> datatypeDescriptions = new ArrayList<BiomobyDatatypeDescription>(); - for (MobyDataType datatype : datatypes) { - BiomobyDatatypeDescription dataDesc = new BiomobyDatatypeDescription(); - dataDesc.setAuthorityName(datatype.getAuthority()); - dataDesc.setDatatypeName(datatype.getName()); - dataDesc.setEmailContact(datatype.getEmailContact()); - dataDesc.setEndpoint(URI.create(registryEndpoint)); - dataDesc.setNamespace(URI.create(registryNamespace)); - dataDesc.setParent(datatype.getParentName()); - dataDesc.setDescription(datatype.getDescription()); - String lsid = datatype.getLSID(); - if (lsid != null && lsid.length() > 0) { - try { - dataDesc.setLsid(URI.create(lsid)); - } catch (Exception e) { - - } - } - ArrayList<String> lineage = new ArrayList<String>(); - if (datatype.getParent() == null && !datatype.getName().equals("Object")) { - lineage.add("Object"); - lineage.add(datatype.getName()); - } else - for (MobyDataType d : datatype.getLineage()) - if (!d.getName().equals(datatype.getName())) - lineage.add(d.getName()); - dataDesc.setLineage(lineage.toArray(new String[]{})); - datatypeDescriptions.add(dataDesc); - } - return datatypeDescriptions; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/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 deleted file mode 100644 index 37d677e..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java +++ /dev/null @@ -1,568 +0,0 @@ -/******************************************************************************* - * 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; -import java.io.BufferedReader; -import java.io.File; -import java.io.FileOutputStream; -import java.io.FileReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.PrintWriter; -import java.net.ConnectException; -import java.net.HttpURLConnection; -import java.net.URL; -import java.util.Comparator; - -import org.apache.log4j.Logger; -import org.biomoby.shared.MobyException; - -/** - * An implementation of {@link org.biomoby.shared.CentralAll}, allowing to - * cache locally results of the cumulative methods so it does not need to access - * Moby registry all the time. The other methods of the Central interface do not - * 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 $ - */ - -public class CacheImpl { - - private static Logger log = Logger.getLogger(CacheImpl.class); - - // filename for a list of cached entities - protected static final String LIST_FILE = "__L__S__I__D__S__"; - - /** An ID used in {@link #removeFromCache} indicating data types part. */ - public static final String CACHE_PART_DATATYPES = "c1"; - - /** An ID used in {@link #removeFromCache} indicating services part. */ - public static final String CACHE_PART_SERVICES = "c2"; - - public static final String CACHE_PROP_NAME = "cache-name"; - - public static final String CACHE_PROP_COUNT = "cache-count"; - - public static final String CACHE_PROP_OLDEST = "cache-oldest"; - - public static final String CACHE_PROP_YOUNGEST = "cache-youngest"; - - public static final String CACHE_PROP_SIZE = "cache-size"; - - public static final String CACHE_PROP_LOCATION = "cache-loc"; - - // DEFAULT registry - private String MOBYCENTRAL_REGISTRY_URL = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";; - - // Default Endpoint - private String MOBYCENTRAL_REGISTRY_URI = "http://moby.ucalgary.ca/MOBY/Central";; - - // cache location - private String cacheDir; // as defined in the constructor - - protected File dataTypesCache; - - protected File servicesCache; - - public static final String SERVICE_INSTANCE_FILENAME = "SERVICE_INSTANCE.rdf"; - - private String serviceInstanceRDFLocation = SERVICE_INSTANCE_FILENAME; - - public static final String DATATYPE_FILENAME = "DATATYPES.rdf"; - - private String datatypeRDFLocation = DATATYPE_FILENAME; - - // for optimalization - private String fileSeparator; - - /*************************************************************************** - * Create an instance that will access a default Moby registry and will - * cache results in the 'cacheDir' directory. - * <p> - **************************************************************************/ - public CacheImpl(String cacheDir) throws MobyException { - this(null, null, cacheDir); - } - - /*************************************************************************** - * Create an instance that will access a Moby registry defined by its - * 'endpoint' and 'namespace', and will cache results in the 'cacheDir' - * directory. Note that the same 'cacheDir' can be safely used for more Moby - * registries. - * <p> - **************************************************************************/ - public CacheImpl(String endpoint, String namespace, String cacheDir) - throws MobyException { - if (endpoint != null && !endpoint.trim().equals("")) - this.MOBYCENTRAL_REGISTRY_URL = endpoint; - if (namespace != null && !namespace.trim().equals("")) - this.MOBYCENTRAL_REGISTRY_URI = namespace; - fileSeparator = System.getProperty("file.separator"); - this.cacheDir = cacheDir; - initCache(); - } - - // it makes all necessary directories for cache given in the - // constructor (which is now in global 'cacheDir'); it is - // separated here because it can be called either from the - // constructor, or everytime a cache is going to be used but it is - // not there (somebody removed it) - protected void initCache() throws MobyException { - if (cacheDir != null) { - File cache = createCacheDir(cacheDir, MOBYCENTRAL_REGISTRY_URL); - dataTypesCache = createSubCacheDir(cache, "datatype_rdf"); - servicesCache = createSubCacheDir(cache, "service_rdf"); - serviceInstanceRDFLocation = servicesCache.getPath() - + fileSeparator + SERVICE_INSTANCE_FILENAME; - datatypeRDFLocation = dataTypesCache.getPath() + fileSeparator - + DATATYPE_FILENAME; - } - } - - /*************************************************************************** - * 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() { - return cacheDir; - } - - /*************************************************************************** - * Removes object groups from the cache. If 'id' is null it removes the - * 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}, - * {@link #CACHE_PART_SERVICETYPES}, and {@link - * #CACHE_PART_NAMESPACES}. - **************************************************************************/ - public void removeFromCache(String id) { - try { - if (cacheDir != null) { - String[] parts = null; - if (id == null) - parts = new String[] { "datatype_rdf", "service_rdf" }; - else if (id.equals(CACHE_PART_SERVICES)) - parts = new String[] { "service_rdf" }; - else if (id.equals(CACHE_PART_DATATYPES)) - parts = new String[] { "datatype_rdf" }; - if (parts != null) { - removeCacheDir(cacheDir, MOBYCENTRAL_REGISTRY_URL, parts); - } - } - } catch (MobyException e) { - log.error("Removing cache failed: " + e.getMessage()); - } - } - - /** - * 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. - */ - protected File createCacheDir(String cacheDirectory, String registryId) - throws MobyException { - if (registryId == null || registryId.equals("")) - registryId = MOBYCENTRAL_REGISTRY_URL; - File cache = new File(cacheDirectory + fileSeparator - + clean(registryId)); - try { - if (!cache.exists()) - if (!cache.mkdirs()) - throw new MobyException("Cannot create '" - + cache.getAbsolutePath() + "'."); - if (!cache.isDirectory()) - throw new MobyException("Cache location '" - + cache.getAbsolutePath() - + "' exists but it is not a directory."); - if (!cache.canWrite()) - throw new MobyException("Cache location '" - + cache.getAbsolutePath() + "' is not writable for me."); - return cache; - } catch (SecurityException e) { - throw new MobyException("Cannot handle cache location '" - + cache.getAbsolutePath() + "'. " + e.toString()); - } - } - - /** - * Remove cache and all (but given in 'subCacheDirNames') its - * subdirectories. - */ - protected void removeCacheDir(String cacheDirectory, String registryId, - String[] subCacheDirNames) throws MobyException { - if (registryId == null || registryId.equals("")) - registryId = MOBYCENTRAL_REGISTRY_URL; - File cache = new File(cacheDirectory + fileSeparator - + clean(registryId)); - try { - if (!cache.exists()) - return; - if (!cache.isDirectory()) - throw new MobyException("Cache location '" - + cache.getAbsolutePath() - + "' exists but it is not a directory."); - if (!cache.canWrite()) - throw new MobyException("Cache location '" - + cache.getAbsolutePath() + "' is not writable for me."); - for (int i = 0; i < subCacheDirNames.length; i++) { - File cacheSubDir = new File(cache.getAbsolutePath() - + fileSeparator + clean(subCacheDirNames[i])); - File[] files = cacheSubDir.listFiles(); - for (int f = 0; f < files.length; f++) { - if (files[f].isDirectory()) - throw new MobyException("Found a directory '" - + files[f].getAbsolutePath() - + "' where no directory should be"); - if (!files[f].delete()) - log.error("Can't delete file '" + files[f] + "'."); - } - cacheSubDir.delete(); - } - cache.delete(); - - } catch (SecurityException e) { - throw new MobyException("Cannot handle cache location '" - + cache.getAbsolutePath() + "'. " + e.toString()); - } - } - - // - protected File createSubCacheDir(File mainCache, String subCacheDirName) - throws MobyException { - File cache = new File(mainCache.getAbsolutePath() + fileSeparator - + clean(subCacheDirName)); - try { - if (!cache.exists()) - if (!cache.mkdirs()) - throw new MobyException("Cannot create '" - + cache.getAbsolutePath() + "'."); - return cache; - } catch (SecurityException e) { - throw new MobyException("Cannot handle cache location '" - + cache.getAbsolutePath() + "'. " + e.toString()); - } - } - - /*************************************************************************** - * Replace non digit/letter characters in 'toBeCleaned' by their numeric - * value. If there are more such numeric values side by side, put a dot - * between them. Return the cleaned string. - **************************************************************************/ - protected static String clean(String toBeCleaned) { - - char[] chars = toBeCleaned.toCharArray(); - int len = chars.length; - int i = -1; - while (++i < len) { - char c = chars[i]; - if (!Character.isLetterOrDigit(c) && c != '_') - break; - } - if (i < len) { - StringBuffer buf = new StringBuffer(len * 2); - for (int j = 0; j < i; j++) { - buf.append(chars[j]); - } - boolean lastOneWasDigitalized = false; - while (i < len) { - char c = chars[i]; - if (Character.isLetterOrDigit(c) || c == '_') { - buf.append(c); - lastOneWasDigitalized = false; - } else { - if (lastOneWasDigitalized) - buf.append('.'); - buf.append((int) c); - lastOneWasDigitalized = true; - } - i++; - } - return new String(buf); - } - return toBeCleaned; - } - - // create a file and put into it data to be cached - protected static void store(File cache, String name, String data) - throws MobyException { - // File outputFile = new File (cache.getAbsolutePath() + fileSeparator + - // clean (name)); - File outputFile = new File(cache.getAbsolutePath() - + System.getProperty("file.separator") + name); - try { - PrintWriter fileout = new PrintWriter(new BufferedOutputStream( - new FileOutputStream(outputFile))); - fileout.write(data); - fileout.close(); - } catch (IOException e) { - throw new MobyException("Cannot write to '" - + outputFile.getAbsolutePath() + ". " + e.toString()); - } - } - - // create a file from a url - protected void storeURL(File cache, String name, String url) - throws MobyException { - File outputFile = new File(cache.getAbsolutePath() + fileSeparator - + name); - try { - StringBuffer sb = new StringBuffer(); - String newline = System.getProperty("line.separator"); - HttpURLConnection urlConnection = null; - - URL rdf_url = new URL(url); - urlConnection = (HttpURLConnection) rdf_url.openConnection(); - urlConnection.setDefaultUseCaches(false); - 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; - while ((inputLine = in.readLine()) != null) - sb.append(inputLine + newline); - in.close(); - - PrintWriter fileout = new PrintWriter(new BufferedOutputStream( - new FileOutputStream(outputFile))); - fileout.write(sb.toString()); - fileout.close(); - } catch (ConnectException e) { - throw new MobyException("Cannot read from url '" - + url + "'. " + e.toString()); - } catch (IOException e) { - throw new MobyException("Cannot write to '" - + outputFile.getAbsolutePath() + "'. " + e.toString()); - } catch (Exception e) { - throw new MobyException("Unexpected Exception caught: " + e.toString()); - } - } - - // remove a file from a cache - protected void remove(File cache, String name) { - File file = new File(cache, name); - // do not throw here an exception because a missing file - // can be a legitimate status (e.g. for LIST_FILE when we - // are updating) - file.delete(); - } - - /*************************************************************************** - * Read a cached file - **************************************************************************/ - protected static String load(File file) throws MobyException { - try { - StringBuffer buf = new StringBuffer(); - BufferedReader in = new BufferedReader(new FileReader(file)); - char[] buffer = new char[1024]; - int charsRead; - - while ((charsRead = in.read(buffer, 0, 1024)) != -1) { - buf.append(buffer, 0, charsRead); - } - - return new String(buf); - - } catch (Throwable e) { // be prepare for "out-of-memory" error - throw new MobyException("Serious error when reading from cache. " - + e.toString()); - - } - } - - /*************************************************************************** - * Is the given cache empty (meaning: cache directory does not exist, is - * empty, or contains only files to be ignored)? - **************************************************************************/ - protected boolean isCacheEmpty(File cache) throws MobyException { - if (cache == null) - return true; - String[] list = cache.list(); - if (list == null || list.length == 0) - return true; - for (int i = 0; i < list.length; i++) { - if (!ignoredForEmptiness(new File(list[i]))) - return false; - } - return true; - } - - /*************************************************************************** - * A LIST_FILE is a TOC of a cache object (each cache part has its own - * LIST_FILE). Read it and return it. If it does not exist, return null. - **************************************************************************/ - protected static String getListFile(File cache) throws MobyException { - File listFile = new File(cache, LIST_FILE); - if (!listFile.exists()) - return null; - return load(listFile); - } - - /*************************************************************************** - * A LIST_FILE is a TOC of a cache object (each cache part has its own - * LIST_FILE). Read it and return it. If it does not exist, return null. - **************************************************************************/ - protected static void storeListFile(File cache, String data) - throws MobyException { - CacheImpl.store(cache, LIST_FILE, data); - } - - /*************************************************************************** - * Return a comparator for Files that compares in case-insensitive way. - **************************************************************************/ - protected static Comparator getFileComparator() { - return new Comparator() { - public int compare(Object o1, Object o2) { - return o1.toString().compareToIgnoreCase(o2.toString()); - } - }; - } - - /*************************************************************************** - * Some file (when being read from a cache directory) are ignored. - **************************************************************************/ - protected static boolean ignored(File file) { - String path = file.getPath(); - return path.endsWith("~") || path.endsWith(LIST_FILE); - } - - /*************************************************************************** - * Some file (when a cache is being tested fir emptyness) are ignored. - **************************************************************************/ - protected static boolean ignoredForEmptiness(File file) { - String path = file.getPath(); - return path.endsWith("~"); - } - - /*************************************************************************** - * - **************************************************************************/ - protected static String MSG_CACHE_NOT_DIR(File cache) { - return "Surprisingly, '" + cache.getAbsolutePath() - + "' is not a directory. Strange..."; - } - - /*************************************************************************** - * - **************************************************************************/ - protected static String MSG_CACHE_BAD_FILE(File file, Exception e) { - return "Ignoring '" + file.getPath() - + "'. It should not be in the cache directory:" - + e.getMessage(); - } - - /*************************************************************************** - * 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) - **************************************************************************/ - public long getCacheAge() { - try { - long dataTypesCacheAge = (isCacheEmpty(dataTypesCache) ? Long.MAX_VALUE - : dataTypesCache.lastModified()); - long servicesCacheAge = (isCacheEmpty(servicesCache) ? Long.MAX_VALUE - : servicesCache.lastModified()); - long age = Math.min(dataTypesCacheAge, servicesCacheAge); - return (age == Long.MAX_VALUE ? -1 : age); - } catch (MobyException e) { - return -1; - } - } - - /** - * @return the serviceInstanceRDFLocation - */ - public String getServiceInstanceRDFLocation() { - return serviceInstanceRDFLocation; - } - - /** - * @param serviceInstanceRDFLocation - * the serviceInstanceRDFLocation to set - */ - public void setServiceInstanceRDFLocation(String serviceInstanceRDFLocation) { - this.serviceInstanceRDFLocation = serviceInstanceRDFLocation; - } - - /** - * @return the mOBYCENTRAL_REGISTRY_URI - */ - public String getMOBYCENTRAL_REGISTRY_URI() { - return MOBYCENTRAL_REGISTRY_URI; - } - - /** - * @param mobycentral_registry_uri - * the mOBYCENTRAL_REGISTRY_URI to set - */ - public void setMOBYCENTRAL_REGISTRY_URI(String mobycentral_registry_uri) { - MOBYCENTRAL_REGISTRY_URI = mobycentral_registry_uri; - } - - /** - * @return the MOBYCENTRAL_REGISTRY_URL - */ - public String getMOBYCENTRAL_REGISTRY_URL() { - return MOBYCENTRAL_REGISTRY_URL; - } - - /** - * @param mobycentral_registry_url - * the MOBYCENTRAL_REGISTRY_URL to set - */ - public void setMOBYCENTRAL_REGISTRY_URL(String mobycentral_registry_url) { - MOBYCENTRAL_REGISTRY_URL = mobycentral_registry_url; - } - - /** - * @return the datatypeRDFLocation - */ - public String getDatatypeRDFLocation() { - return datatypeRDFLocation; - } - - /** - * @param datatypeRDFLocation the datatypeRDFLocation to set - */ - public void setDatatypeRDFLocation(String datatypeRDFLocation) { - this.datatypeRDFLocation = datatypeRDFLocation; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceDescription.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceDescription.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceDescription.java deleted file mode 100644 index f327e96..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceDescription.java +++ /dev/null @@ -1,137 +0,0 @@ -package net.sf.taverna.t2.activities.biomoby.servicedescriptions; - -import java.net.URI; -import java.util.Arrays; -import java.util.List; - -import javax.swing.Icon; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean; -import net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon; -import net.sf.taverna.t2.servicedescriptions.ServiceDescription; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; - -public class BiomobyServiceDescription extends - ServiceDescription<BiomobyActivityConfigurationBean> { - - private String authorityName; - private String category; - private String emailContact; - private URI endpoint; - - private URI lsid; - - private URI namespace; - private String serviceName; - private String serviceType; - private URI signatureURI; - - @Override - public Class<? extends Activity<BiomobyActivityConfigurationBean>> getActivityClass() { - return BiomobyActivity.class; - } - - @Override - public BiomobyActivityConfigurationBean getActivityConfiguration() { - BiomobyActivityConfigurationBean bean = new BiomobyActivityConfigurationBean(); - bean.setAuthorityName(getAuthorityName()); - bean.setServiceName(getServiceName()); - bean.setMobyEndpoint(getEndpoint().toASCIIString()); - return bean; - } - - public String getAuthorityName() { - return authorityName; - } - - public String getCategory() { - return category; - } - - public String getEmailContact() { - return emailContact; - } - - public URI getEndpoint() { - return endpoint; - } - - @Override - public Icon getIcon() { - return BiomobyActivityIcon.getBiomobyIcon(); - } - - public URI getLSID() { - return lsid; - } - - @Override - public String getName() { - return getServiceName(); - } - - public URI getNamespace() { - return namespace; - } - - @Override - public List<String> getPath() { - return Arrays.asList("Biomoby @ " + getEndpoint(), getServiceType(), getAuthorityName()); - } - - public String getServiceName() { - return serviceName; - } - - public String getServiceType() { - return serviceType; - } - - public URI getSignatureURI() { - return signatureURI; - } - - public void setAuthorityName(String authorityName) { - this.authorityName = authorityName; - } - - public void setCategory(String category) { - this.category = category; - } - - public void setEmailContact(String emailContact) { - this.emailContact = emailContact; - } - - public void setEndpoint(URI endpoint) { - this.endpoint = endpoint; - } - - public void setLSID(URI lsid) { - this.lsid = lsid; - } - - public void setNamespace(URI namespace) { - this.namespace = namespace; - } - - public void setServiceName(String serviceName) { - this.serviceName = serviceName; - } - - public void setServiceType(String serviceType) { - this.serviceType = serviceType; - } - - public void setSignatureURI(URI signatureURI) { - this.signatureURI = signatureURI; - } - - @Override - protected List<Object> getIdentifyingData() { - return Arrays.<Object>asList(getNamespace(), getEndpoint(), getAuthorityName(), getServiceName()); - } - - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java deleted file mode 100644 index a80c5fb..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java +++ /dev/null @@ -1,121 +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.biomoby.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.activities.biomoby.query.BiomobyActivityIcon; -import net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper; -import net.sf.taverna.t2.activities.biomoby.ui.AddBiomobyDialogue; -import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider; -import net.sf.taverna.t2.servicedescriptions.CustomizedConfigurePanelProvider; -import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry; - -import org.biomoby.client.CentralImpl; -import org.biomoby.shared.MobyException; - -public class BiomobyServiceProvider extends - AbstractConfigurableServiceProvider<BiomobyServiceProviderConfig> implements - CustomizedConfigurePanelProvider<BiomobyServiceProviderConfig> { - - private static final URI providerId = URI - .create("http://taverna.sf.net/2010/service-provider/biomoby";); - private ServiceDescriptionRegistry serviceDescriptionRegistry; - - public BiomobyServiceProvider() { - super(new BiomobyServiceProviderConfig()); - } - - public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) { - try { - // constructor throws exception if it cannot communicate - // with the registry - BiomobyQueryHelper helper = new BiomobyQueryHelper(getConfiguration().getEndpoint() - .toASCIIString(), getConfiguration().getNamespace().toASCIIString()); - helper.findServiceDescriptionsAsync(callBack); - } catch (MobyException ex) { - callBack.fail("Could not connect to Biomoby endpoint " - + getConfiguration().getEndpoint(), ex); - } - } - - @Override - public List<BiomobyServiceProviderConfig> getDefaultConfigurations() { - - List<BiomobyServiceProviderConfig> defaults = new ArrayList<BiomobyServiceProviderConfig>(); - - // If defaults have failed to load from a configuration file then load them here. - if (!serviceDescriptionRegistry.isDefaultSystemConfigurableProvidersLoaded()) { - defaults.add(new BiomobyServiceProviderConfig(CentralImpl.DEFAULT_ENDPOINT, - CentralImpl.DEFAULT_NAMESPACE)); - } // else return an empty list - - return defaults; - } - - public String getName() { - return "Biomoby service"; - } - - public Icon getIcon() { - return BiomobyActivityIcon.getBiomobyIcon(); - } - - @Override - public String toString() { - return getName() + " " + getConfiguration().getEndpoint(); - } - - @SuppressWarnings("serial") - public void createCustomizedConfigurePanel( - final CustomizedConfigureCallBack<BiomobyServiceProviderConfig> callBack) { - AddBiomobyDialogue addBiomobyDialogue = new AddBiomobyDialogue() { - @Override - protected void addRegistry(String registryEndpoint, String registryURI) { - BiomobyServiceProviderConfig providerConfig = new BiomobyServiceProviderConfig( - registryEndpoint, registryURI); - callBack.newProviderConfiguration(providerConfig); - } - }; - addBiomobyDialogue.setVisible(true); - } - - @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/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProviderConfig.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProviderConfig.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProviderConfig.java deleted file mode 100644 index 3f568c7..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProviderConfig.java +++ /dev/null @@ -1,37 +0,0 @@ -package net.sf.taverna.t2.activities.biomoby.servicedescriptions; - -import java.net.URI; - -import net.sf.taverna.t2.lang.beans.PropertyAnnotated; - -public class BiomobyServiceProviderConfig extends PropertyAnnotated { - - private URI endpoint; - - private URI namespace; - - public BiomobyServiceProviderConfig() { - } - - public BiomobyServiceProviderConfig(String endpoint, String namespace) { - this.endpoint = URI.create(endpoint.trim()); - this.namespace = URI.create(namespace.trim()); - } - - public URI getEndpoint() { - return endpoint; - } - - public URI getNamespace() { - return namespace; - } - - public void setEndpoint(URI endpoint) { - this.endpoint = endpoint; - } - - public void setNamespace(URI namespace) { - this.namespace = namespace; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/AddBiomobyDialogue.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/AddBiomobyDialogue.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/AddBiomobyDialogue.java deleted file mode 100644 index 99b82f9..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/AddBiomobyDialogue.java +++ /dev/null @@ -1,94 +0,0 @@ -package net.sf.taverna.t2.activities.biomoby.ui; - -import java.awt.event.ActionEvent; - -import javax.swing.AbstractAction; -import javax.swing.JButton; - -import net.sf.taverna.t2.activities.biomoby.actions.BiomobyScavengerDialog; -import net.sf.taverna.t2.workbench.MainWindow; -import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog; - -import org.apache.log4j.Logger; -import org.biomoby.client.CentralImpl; - -@SuppressWarnings("serial") -public abstract class AddBiomobyDialogue extends HelpEnabledDialog { - - @SuppressWarnings("unused") - private static Logger logger = Logger.getLogger(AddBiomobyDialogue.class); - - private String endpoint = CentralImpl.DEFAULT_ENDPOINT; - - private String uri = CentralImpl.DEFAULT_NAMESPACE; - - public AddBiomobyDialogue() { - super(MainWindow.getMainWindow(), "Add BioMoby Registry", true, null); - initialize(); - setLocationRelativeTo(getParent()); - } - public void initialize() { - final BiomobyScavengerDialog msp = new BiomobyScavengerDialog(); - getContentPane().add(msp); - JButton accept = new JButton(new OKAction(msp)); - JButton cancel = new JButton(new CancelAction()); - msp.add(accept); - msp.add(cancel); - setResizable(false); - getContentPane().add(msp); - setLocationRelativeTo(null); - pack(); - } - - protected abstract void addRegistry(String registryEndpoint, - String registryURI); - - public class CancelAction extends AbstractAction { - public CancelAction() { - super("Cancel"); - } - - public void actionPerformed(ActionEvent ae2) { - if (isVisible()) { - setVisible(false); - dispose(); - } - } - } - - public class OKAction extends AbstractAction { - private final BiomobyScavengerDialog scavengerDialogue; - - private OKAction(BiomobyScavengerDialog msp) { - super("OK"); - this.scavengerDialogue = msp; - } - - public void actionPerformed(ActionEvent ae2) { - if (isVisible()) { - String registryEndpoint = ""; - String registryNamespace = ""; - - if (scavengerDialogue.getRegistryEndpoint().equals("")) { - registryEndpoint = endpoint; - } else { - registryEndpoint = scavengerDialogue.getRegistryEndpoint(); - } - - if (scavengerDialogue.getRegistryEndpoint().equals("")) { - registryNamespace = uri; - } else { - registryNamespace = scavengerDialogue.getRegistryURI(); - } - - try { - addRegistry(registryEndpoint.trim(), registryNamespace.trim()); - } finally { - setVisible(false); - dispose(); - } - } - } - } - -}
