taverna 3 gis activity
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/commit/3ca3856a Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/tree/3ca3856a Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/diff/3ca3856a Branch: refs/heads/master Commit: 3ca3856a4e8183d7652b5a5fef158efaa69cead6 Parents: 9c93062 Author: edikaradumi <[email protected]> Authored: Mon Jul 11 12:26:02 2016 +0100 Committer: Edi Karadumi <[email protected]> Committed: Mon Jul 11 12:36:06 2016 +0100 ---------------------------------------------------------------------- apache-taverna-activity-gis-activity-ui/pom.xml | 105 +++++++++ .../gis/ui/config/GisConfigurationPanel.java | 84 ++++++++ .../gis/ui/config/GisConfigureAction.java | 46 ++++ .../gis/ui/menu/GisConfigureMenuAction.java | 64 ++++++ .../gis/ui/serviceprovider/GisServiceDesc.java | 95 +++++++++ .../gis/ui/serviceprovider/GisServiceIcon.java | 37 ++++ .../ui/serviceprovider/GisServiceProvider.java | 184 ++++++++++++++++ .../ui/view/GisActivityContextViewFactory.java | 59 ++++++ .../taverna/gis/ui/view/GisContextualView.java | 88 ++++++++ .../resources/META-INF/spring/context-osgi.xml | 26 +++ .../main/resources/META-INF/spring/context.xml | 31 +++ .../src/main/resources/exampleIcon.png | Bin 0 -> 541 bytes apache-taverna-activity-gis-activity/pom.xml | 57 +++++ .../org/apache/taverna/gis/GisActivity.java | 157 ++++++++++++++ .../gis/GisActivityConfigurationBean.java | 52 +++++ .../apache/taverna/gis/GisActivityExample.java | 132 ++++++++++++ .../apache/taverna/gis/GisActivityFactory.java | 94 ++++++++ .../taverna/gis/GisActivityHealthChecker.java | 63 ++++++ .../src/main/resources/schema.json | 25 +++ .../src/main/resources/spring/context-osgi.xml | 17 ++ .../src/main/resources/spring/context.xml | 12 ++ .../src/main/resources/wps_config.xml | 212 +++++++++++++++++++ .../taverna/gis/GisActivityFactoryTest.java | 100 +++++++++ .../org/apache/taverna/gis/GisActivityTest.java | 73 +++++++ apache-taverna-activity-gis-plugin/pom.xml | 28 +++ pom.xml | 119 ++++++----- taverna-gis-client/pom.xml | 17 ++ 27 files changed, 1923 insertions(+), 54 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/pom.xml ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/pom.xml b/apache-taverna-activity-gis-activity-ui/pom.xml new file mode 100644 index 0000000..45a1e11 --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/pom.xml @@ -0,0 +1,105 @@ +<?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>org.apache.taverna.gis</groupId> + <artifactId>apache-taverna-activity-gis</artifactId> + <version>0.0.1-incubating.SNAPSHOT</version> + </parent> + <artifactId>apache-taverna-activity-gis-activity-ui</artifactId> + <packaging>bundle</packaging> + <name>Gis Taverna activity UI</name> + + <dependencies> + <dependency> + <groupId>${project.parent.groupId}</groupId> + <artifactId>taverna-gis-client</artifactId> + <version>${project.parent.version}</version> + </dependency> + + <dependency> + <groupId>org.apache.taverna.engine</groupId> + <artifactId>taverna-workflowmodel-api</artifactId> + <version>${taverna.engine.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.engine</groupId> + <artifactId>taverna-reference-api</artifactId> + <version>${taverna.engine.version}</version> + </dependency> + + <dependency> + <groupId>com.fasterxml.jackson.core</groupId> + <artifactId>jackson-databind</artifactId> + <version>2.3.0</version> + </dependency> + + <dependency> + <groupId>junit</groupId> + <artifactId>junit</artifactId> + <version>4.4</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.apache.taverna.engine</groupId> + <artifactId>taverna-workflowmodel-impl</artifactId> + <version>${taverna.engine.version}</version> + <scope>test</scope> + </dependency> + + + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-activity-palette-api</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-edits-api</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-selection-api</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-menu-api</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-activity-icons-api</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-helper-api</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-ui</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-configuration-ui-api</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-contextual-views-api</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.workbench</groupId> + <artifactId>taverna-activity-tools</artifactId> + <version>${taverna.workbench.version}</version> + </dependency> + + </dependencies> +</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigurationPanel.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigurationPanel.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigurationPanel.java new file mode 100644 index 0000000..160adce --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigurationPanel.java @@ -0,0 +1,84 @@ +package org.apache.taverna.gis.ui.config; + +import java.awt.GridLayout; +import java.net.URI; + +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JTextField; + +import org.apache.taverna.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel; + +import org.apache.taverna.services.ServiceRegistry; +import org.apache.taverna.scufl2.api.activity.Activity; + +@SuppressWarnings("serial") +public class GisConfigurationPanel extends ActivityConfigurationPanel { + + private final ServiceRegistry serviceRegistry; + + private JTextField fieldString; + private JTextField fieldURI; + + public GisConfigurationPanel(Activity activity, ServiceRegistry serviceRegistry) { + super(activity); + this.serviceRegistry = serviceRegistry; + initialise(); + } + + protected void initialise() { + // call super.initialise() to initialise the configuration + super.initialise(); + + removeAll(); + setLayout(new GridLayout(0, 2)); + + // FIXME: Create GUI depending on activity configuration bean + JLabel labelString = new JLabel("Example string:"); + add(labelString); + fieldString = new JTextField(20); + add(fieldString); + labelString.setLabelFor(fieldString); + + JLabel labelURI = new JLabel("Example URI:"); + add(labelURI); + fieldURI = new JTextField(25); + add(fieldURI); + labelURI.setLabelFor(fieldURI); + + // Populate fields from activity configuration + fieldString.setText(getProperty("exampleString")); + fieldURI.setText(getProperty("exampleUri")); + } + + /** + * Check that user values in UI are valid + */ + @Override + public boolean checkValues() { + try { + URI.create(fieldURI.getText()); + } catch (IllegalArgumentException ex) { + JOptionPane.showMessageDialog(this, ex.getCause().getMessage(), + "Invalid URI", JOptionPane.ERROR_MESSAGE); + // Not valid, return false + return false; + } + // All valid, return true + return true; + } + + /** + * Set the configuration properties from the UI + */ + @Override + public void noteConfiguration() { + // FIXME: Update bean fields from your UI elements + setProperty("exampleString", fieldString.getText()); + setProperty("exampleUri", fieldURI.getText()); + + configureInputPorts(serviceRegistry); + configureOutputPorts(serviceRegistry); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigureAction.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigureAction.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigureAction.java new file mode 100644 index 0000000..32ea030 --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigureAction.java @@ -0,0 +1,46 @@ +package org.apache.taverna.gis.ui.config; + +import java.awt.event.ActionEvent; + +import org.apache.taverna.services.ServiceRegistry; +import org.apache.taverna.scufl2.api.activity.Activity; + +import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry; +import org.apache.taverna.workbench.activityicons.ActivityIconManager; +import org.apache.taverna.workbench.edits.EditManager; +import org.apache.taverna.workbench.file.FileManager; +import org.apache.taverna.workbench.ui.actions.activity.ActivityConfigurationAction; +import org.apache.taverna.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog; + +@SuppressWarnings("serial") +public class GisConfigureAction extends ActivityConfigurationAction { + + private final EditManager editManager; + private final FileManager fileManager; + private final ServiceRegistry serviceRegistry; + + public GisConfigureAction(Activity activity, + EditManager editManager, FileManager fileManager, + ActivityIconManager activityIconManager, + ServiceDescriptionRegistry serviceDescriptionRegistry, + ServiceRegistry serviceRegistry) { + super(activity, activityIconManager, serviceDescriptionRegistry); + this.editManager = editManager; + this.fileManager = fileManager; + this.serviceRegistry = serviceRegistry; + } + + public void actionPerformed(ActionEvent e) { + ActivityConfigurationDialog currentDialog = getDialog(getActivity()); + if (currentDialog != null) { + currentDialog.toFront(); + return; + } + + GisConfigurationPanel panel = new GisConfigurationPanel(getActivity(), serviceRegistry); + ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(), panel, editManager); + + setDialog(getActivity(), dialog, fileManager); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/menu/GisConfigureMenuAction.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/menu/GisConfigureMenuAction.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/menu/GisConfigureMenuAction.java new file mode 100644 index 0000000..cdf45dc --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/menu/GisConfigureMenuAction.java @@ -0,0 +1,64 @@ +package org.apache.taverna.gis.ui.menu; + +import java.net.URI; + +import javax.swing.Action; + +import org.apache.taverna.services.ServiceRegistry; + +import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry; +import org.apache.taverna.ui.menu.ContextualMenuComponent; +import org.apache.taverna.ui.menu.MenuComponent; +import org.apache.taverna.workbench.activityicons.ActivityIconManager; +import org.apache.taverna.workbench.activitytools.AbstractConfigureActivityMenuAction; +import org.apache.taverna.workbench.edits.EditManager; +import org.apache.taverna.workbench.file.FileManager; + +import org.apache.taverna.gis.ui.config.GisConfigureAction; + +public class GisConfigureMenuAction extends AbstractConfigureActivityMenuAction implements + MenuComponent, ContextualMenuComponent { + + private static final URI ACTIVITY_TYPE = URI + .create("http://example.com/2013/activity/apache-taverna-activity-gis";); + + private EditManager editManager; + private FileManager fileManager; + private ActivityIconManager activityIconManager; + private ServiceDescriptionRegistry serviceDescriptionRegistry; + private ServiceRegistry serviceRegistry; + + public GisConfigureMenuAction() { + super(ACTIVITY_TYPE); + } + + @Override + protected Action createAction() { + Action result = new GisConfigureAction(findActivity(), editManager, fileManager, + activityIconManager, serviceDescriptionRegistry, serviceRegistry); + result.putValue(Action.NAME, "Configure example service"); + addMenuDots(result); + return result; + } + + 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; + } + + public void setServiceRegistry(ServiceRegistry serviceRegistry) { + this.serviceRegistry = serviceRegistry; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceDesc.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceDesc.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceDesc.java new file mode 100644 index 0000000..5361629 --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceDesc.java @@ -0,0 +1,95 @@ +package org.apache.taverna.gis.ui.serviceprovider; + +import java.net.URI; +import java.util.Arrays; +import java.util.List; + +import javax.swing.Icon; + +import org.apache.taverna.scufl2.api.configurations.Configuration; +import org.apache.taverna.servicedescriptions.ServiceDescription; + +import com.fasterxml.jackson.databind.node.ObjectNode; + +public class GisServiceDesc extends ServiceDescription { + public static final URI ACTIVITY_TYPE = URI + .create("http://ns.taverna.org.uk/2016/activity/gis";); + + + /** + * The type of Activity which should be instantiated when adding a service + * for this description + */ + @Override + public URI getActivityType() { + return ACTIVITY_TYPE; + } + + @Override + public Configuration getActivityConfiguration() { + Configuration configuration = new Configuration(); + configuration.setType(ACTIVITY_TYPE.resolve("#Config")); + ObjectNode json = configuration.getJsonAsObjectNode(); + json.put("ogcServiceUri", ogcServiceUri.toASCIIString()); + json.put("processIdentifier", processIdentifier); + return configuration; + } + + /** + * An icon to represent this service description in the service palette. + */ + @Override + public Icon getIcon() { + return GisServiceIcon.getIcon(); + } + + /** + * The display name that will be shown in service palette and will + * be used as a template for processor name when added to workflow. + */ + @Override + public String getName() { + return processIdentifier; + } + + /** + * The path to this service description in the service palette. Folders + * will be created for each element of the returned path. + */ + @Override + public List<String> getPath() { + // For deeper paths you may return several strings + return Arrays.asList("GIS", "WPS " + getOgcServiceUri()); + } + + /** + * Return a list of data values uniquely identifying this service + * description (to avoid duplicates). Include only primary key like fields, + * ie. ignore descriptions, icons, etc. + */ + @Override + protected List<? extends Object> getIdentifyingData() { + // FIXME: Use your fields instead of example fields + return Arrays.<Object>asList(ogcServiceUri, processIdentifier); + } + + + // All fields are searchable in the Service palette, + // for instance try a search for exampleString:3 + private URI ogcServiceUri; + private String processIdentifier; + + public URI getOgcServiceUri() { + return ogcServiceUri; + } + public void setOgcServiceUri(URI ogcServiceUri) { + this.ogcServiceUri = ogcServiceUri; + } + public String getProcessIdentifier() { + return processIdentifier; + } + public void setProcessIdentifier(String processIdentifier) { + this.processIdentifier = processIdentifier; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceIcon.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceIcon.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceIcon.java new file mode 100644 index 0000000..5f56537 --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceIcon.java @@ -0,0 +1,37 @@ +package org.apache.taverna.gis.ui.serviceprovider; + +import java.net.URI; + +import javax.swing.Icon; +import javax.swing.ImageIcon; + +import org.apache.taverna.workbench.activityicons.ActivityIconSPI; + +public class GisServiceIcon implements ActivityIconSPI { + + private static final URI ACTIVITY_TYPE = URI + .create("http://example.com/2013/activity/apache-taverna-activity-gis";); + + private static Icon icon; + + @Override + public int canProvideIconScore(URI activityType) { + if (ACTIVITY_TYPE.equals(activityType)) { + return DEFAULT_ICON + 1; + } + return NO_ICON; + } + + @Override + public Icon getIcon(URI activityType) { + return getIcon(); + } + + public static Icon getIcon() { + if (icon == null) { + icon = new ImageIcon(GisServiceIcon.class.getResource("/exampleIcon.png")); + } + return icon; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceProvider.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceProvider.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceProvider.java new file mode 100644 index 0000000..13ad4b2 --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceProvider.java @@ -0,0 +1,184 @@ +package org.apache.taverna.gis.ui.serviceprovider; + +import java.io.IOException; +import java.net.URI; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import javax.swing.Icon; + +import org.apache.taverna.scufl2.api.common.Visitor; +import org.apache.taverna.scufl2.api.common.WorkflowBean; +import org.apache.taverna.scufl2.api.configurations.Configuration; +import org.apache.taverna.servicedescriptions.AbstractConfigurableServiceProvider; +import org.apache.taverna.servicedescriptions.ConfigurableServiceProvider; +import org.apache.taverna.servicedescriptions.ServiceDescription; +import org.apache.taverna.servicedescriptions.ServiceDescriptionProvider; +import org.apache.taverna.servicedescriptions.ServiceDescriptionProvider.FindServiceDescriptionsCallBack; +import org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean; +import org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean; +import org.n52.wps.client.WPSClientSession; + +import com.fasterxml.jackson.databind.node.ObjectNode; + +import net.opengis.wps.x100.InputDescriptionType; +import net.opengis.wps.x100.OutputDescriptionType; +import net.opengis.wps.x100.ProcessDescriptionType; + +public class GisServiceProvider extends AbstractConfigurableServiceProvider + implements ConfigurableServiceProvider { + + + public GisServiceProvider() { + super(defaultConfig()); + + } + + private static Configuration defaultConfig() { + Configuration c = new Configuration(); + ObjectNode conf = c.getJsonAsObjectNode(); + conf.put("osgiServiceUri", "http://localhost:8080/geoserver/ows";); + conf.put("processIdentifier", "gs:StringConcatWPS"); + return c; + } + + private static final URI providerId = GisServiceDesc.ACTIVITY_TYPE.resolve("#provider"); + + /** + * Do the actual search for services. Return using the callBack parameter. + */ + @SuppressWarnings("unchecked") + public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) { + // Use callback.status() for long-running searches + callBack.status("Resolving GIS services"); + + List<ServiceDescription> results = new ArrayList<ServiceDescription>(); + + // FIXME: Implement the actual service search/lookup instead + // of dummy for-loop + + GisServiceDesc service = new GisServiceDesc(); + // Populate the service description bean + ObjectNode conf = getConfiguration().getJsonAsObjectNode(); + String serviceUri = conf.get("osgiServiceUri").asText(); + service.setOgcServiceUri(URI.create(serviceUri)); + String processIdentifier = conf.get("processIdentifier").asText(); + service.setProcessIdentifier(processIdentifier); + + // TODO: Optional: set description (Set a better description + service.setDescription(processIdentifier); + + // TODO: Exctract in a separate method + // Get input ports + + WPSClientSession wpsClient = WPSClientSession.getInstance(); + + ProcessDescriptionType processDescription; + try { + processDescription = wpsClient + .getProcessDescription(serviceUri, processIdentifier); + + InputDescriptionType[] inputList = processDescription.getDataInputs() + .getInputArray(); + + List<ActivityInputPortDefinitionBean> inputPortDefinitions = new ArrayList<ActivityInputPortDefinitionBean>(); + + for (InputDescriptionType input : inputList) { + ActivityInputPortDefinitionBean newInputPort = new ActivityInputPortDefinitionBean(); + newInputPort.setName(input.getIdentifier().getStringValue()); + newInputPort.setDepth(0); + newInputPort.setAllowsLiteralValues(true); + newInputPort.setHandledReferenceSchemes(null); + newInputPort.setTranslatedElementType(String.class); + + inputPortDefinitions.add(newInputPort); + + } + + // service.setInputPortDefinitions(inputPortDefinitions); + + + // Get output ports + + OutputDescriptionType[] outputList = processDescription.getProcessOutputs().getOutputArray(); + List<ActivityOutputPortDefinitionBean> outputPortDefinitions = new ArrayList<ActivityOutputPortDefinitionBean>(); + + for( OutputDescriptionType output : outputList ) + { + ActivityOutputPortDefinitionBean newOutputPort = new ActivityOutputPortDefinitionBean(); + newOutputPort.setName(output.getIdentifier().getStringValue()); + newOutputPort.setDepth(0); + + outputPortDefinitions.add(newOutputPort); + + } + + //service.setOutputPortDefinitions(outputPortDefinitions); + + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + results.add(service); + + // partialResults() can also be called several times from inside + // for-loop if the full search takes a long time + callBack.partialResults(results); + + // No more results will be coming + callBack.finished(); + } + + /** + * Icon for service provider + */ + public Icon getIcon() { + return GisServiceIcon.getIcon(); + } + + /** + * Name of service provider, appears in right click for 'Remove service + * provider' + */ + public String getName() { + return "Geospatial Web Services"; + } + + @Override + public String toString() { + return "Geospatial Web Services " + getConfiguration().getJson().get("osgiServiceUri"); + } + + public String getId() { + return providerId.toASCIIString(); + } + + @Override + protected List<? extends Object> getIdentifyingData() { + return Arrays.asList(getConfiguration().getJson().get("osgiServiceUri"), + getConfiguration().getJson().get("processIdentifier")); + } + + @Override + public ServiceDescriptionProvider newInstance() { + return new GisServiceProvider(); + } + + @Override + public URI getType() { + return providerId; + } + + @Override + public void setType(URI type) { + } + + @Override + public boolean accept(Visitor visitor) { + return false; + } + + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisActivityContextViewFactory.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisActivityContextViewFactory.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisActivityContextViewFactory.java new file mode 100644 index 0000000..1a0dc13 --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisActivityContextViewFactory.java @@ -0,0 +1,59 @@ +package org.apache.taverna.gis.ui.view; + +import java.net.URI; +import java.util.Arrays; +import java.util.List; + +import org.apache.taverna.services.ServiceRegistry; +import org.apache.taverna.scufl2.api.activity.Activity; + +import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry; +import org.apache.taverna.workbench.activityicons.ActivityIconManager; +import org.apache.taverna.workbench.edits.EditManager; +import org.apache.taverna.workbench.file.FileManager; +import org.apache.taverna.workbench.ui.views.contextualviews.ContextualView; +import org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory; + +public class GisActivityContextViewFactory implements ContextualViewFactory<Activity> { + + private static final URI ACTIVITY_TYPE = URI + .create("http://example.com/2013/activity/apache-taverna-activity-gis";); + + private EditManager editManager; + private FileManager fileManager; + private ActivityIconManager activityIconManager; + private ServiceDescriptionRegistry serviceDescriptionRegistry; + private ServiceRegistry serviceRegistry; + + @Override + public boolean canHandle(Object object) { + return object instanceof Activity && ((Activity) object).getType().equals(ACTIVITY_TYPE); + } + + @Override + public List<ContextualView> getViews(Activity selection) { + return Arrays.<ContextualView>asList(new GisContextualView(selection, editManager, + fileManager, activityIconManager, serviceDescriptionRegistry, serviceRegistry)); + } + + 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; + } + + public void setServiceRegistry(ServiceRegistry serviceRegistry) { + this.serviceRegistry = serviceRegistry; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisContextualView.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisContextualView.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisContextualView.java new file mode 100644 index 0000000..08fff1f --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisContextualView.java @@ -0,0 +1,88 @@ +package org.apache.taverna.gis.ui.view; + +import java.awt.Frame; + +import javax.swing.Action; +import javax.swing.JComponent; +import javax.swing.JLabel; +import javax.swing.JPanel; + +import com.fasterxml.jackson.databind.JsonNode; + +import org.apache.taverna.services.ServiceRegistry; + +import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry; +import org.apache.taverna.workbench.activityicons.ActivityIconManager; +import org.apache.taverna.workbench.edits.EditManager; +import org.apache.taverna.workbench.file.FileManager; +import org.apache.taverna.workbench.ui.actions.activity.ActivityContextualView; + +import org.apache.taverna.scufl2.api.activity.Activity; + +import org.apache.taverna.gis.ui.config.GisConfigureAction; + +@SuppressWarnings("serial") +public class GisContextualView extends ActivityContextualView { + + private final EditManager editManager; + private final FileManager fileManager; + private final ActivityIconManager activityIconManager; + private final ServiceDescriptionRegistry serviceDescriptionRegistry; + private final ServiceRegistry serviceRegistry; + + private JLabel description = new JLabel("ads"); + + public GisContextualView(Activity activity, EditManager editManager, + FileManager fileManager, ActivityIconManager activityIconManager, + ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) { + super(activity); + this.editManager = editManager; + this.fileManager = fileManager; + this.activityIconManager = activityIconManager; + this.serviceDescriptionRegistry = serviceDescriptionRegistry; + this.serviceRegistry = serviceRegistry; + initView(); + } + + @Override + public JComponent getMainFrame() { + JPanel jPanel = new JPanel(); + jPanel.add(description); + refreshView(); + return jPanel; + } + + @Override + public String getViewTitle() { + JsonNode configuration = getConfigBean().getJson(); + return "Gis service " + configuration.get("exampleString").asText(); + } + + /** + * Typically called when the activity configuration has changed. + */ + @Override + public void refreshView() { + JsonNode configuration = getConfigBean().getJson(); + description.setText("Gis service " + configuration.get("exampleUri").asText() + + " - " + configuration.get("exampleString").asText()); + // TODO: Might also show extra service information looked + // up dynamically from endpoint/registry + } + + /** + * View position hint + */ + @Override + public int getPreferredPosition() { + // We want to be on top + return 100; + } + + @Override + public Action getConfigureAction(final Frame owner) { + return new GisConfigureAction(getActivity(), editManager, fileManager, + activityIconManager, serviceDescriptionRegistry, serviceRegistry); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml b/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml new file mode 100644 index 0000000..4987ea3 --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml @@ -0,0 +1,26 @@ +<?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="GisServiceIcon" interface="org.apache.taverna.workbench.activityicons.ActivityIconSPI" /> + + <service ref="GisServiceProvider" interface="org.apache.taverna.servicedescriptions.ServiceDescriptionProvider" /> + + <service ref="GisConfigureMenuAction" auto-export="interfaces" /> + + <service ref="GisActivityContextViewFactory" interface="org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory" /> + + <reference id="editManager" interface="org.apache.taverna.workbench.edits.EditManager" /> + <reference id="fileManager" interface="org.apache.taverna.workbench.file.FileManager" /> + <reference id="menuManager" interface="org.apache.taverna.ui.menu.MenuManager" /> + <reference id="selectionManager" interface="org.apache.taverna.workbench.selection.SelectionManager" /> + <reference id="activityIconManager" interface="org.apache.taverna.workbench.activityicons.ActivityIconManager" /> + <reference id="colourManager" interface="org.apache.taverna.workbench.configuration.colour.ColourManager" /> + <reference id="serviceDescriptionRegistry" interface="org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry" /> + <reference id="serviceRegistry" interface="org.apache.taverna.services.ServiceRegistry" /> + +</beans:beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context.xml ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context.xml b/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context.xml new file mode 100644 index 0000000..f0c1255 --- /dev/null +++ b/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context.xml @@ -0,0 +1,31 @@ +<?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="GisServiceIcon" + class="org.apache.taverna.gis.ui.serviceprovider.GisServiceIcon" /> + + <bean id="GisServiceProvider" + class="org.apache.taverna.gis.ui.serviceprovider.GisServiceProvider" /> + + <bean id="GisConfigureMenuAction" + class="org.apache.taverna.gis.ui.menu.GisConfigureMenuAction"> + <property name="editManager" ref="editManager" /> + <property name="fileManager" ref="fileManager" /> + <property name="activityIconManager" ref="activityIconManager" /> + <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" /> + <property name="serviceRegistry" ref="serviceRegistry" /> + </bean> + + <bean id="GisActivityContextViewFactory" + class="org.apache.taverna.gis.ui.view.GisActivityContextViewFactory"> + <property name="editManager" ref="editManager" /> + <property name="fileManager" ref="fileManager" /> + <property name="activityIconManager" ref="activityIconManager" /> + <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" /> + <property name="serviceRegistry" ref="serviceRegistry" /> + </bean> + +</beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity-ui/src/main/resources/exampleIcon.png ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity-ui/src/main/resources/exampleIcon.png b/apache-taverna-activity-gis-activity-ui/src/main/resources/exampleIcon.png new file mode 100644 index 0000000..8bb31c3 Binary files /dev/null and b/apache-taverna-activity-gis-activity-ui/src/main/resources/exampleIcon.png differ http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/pom.xml ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/pom.xml b/apache-taverna-activity-gis-activity/pom.xml new file mode 100644 index 0000000..a118bb5 --- /dev/null +++ b/apache-taverna-activity-gis-activity/pom.xml @@ -0,0 +1,57 @@ +<?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>org.apache.taverna.gis</groupId> + <artifactId>apache-taverna-activity-gis</artifactId> + <version>0.0.1-incubating.SNAPSHOT</version> + </parent> + <artifactId>apache-taverna-activity-gis-activity</artifactId> + <packaging>bundle</packaging> + <name>Gis Taverna activity</name> + + <dependencies> + <dependency> + <groupId>org.apache.taverna.engine</groupId> + <artifactId>taverna-workflowmodel-api</artifactId> + <version>${taverna.engine.version}</version> + </dependency> + <dependency> + <groupId>org.apache.taverna.engine</groupId> + <artifactId>taverna-reference-api</artifactId> + <version>${taverna.engine.version}</version> + </dependency> + + <dependency> + <groupId>com.fasterxml.jackson.core</groupId> + <artifactId>jackson-databind</artifactId> + <version>2.3.0</version> + </dependency> + + <dependency> + <groupId>junit</groupId> + <artifactId>junit</artifactId> + <version>4.4</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.apache.taverna.engine</groupId> + <artifactId>taverna-workflowmodel-impl</artifactId> + <version>${taverna.engine.version}</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.apache.taverna.engine</groupId> + <artifactId>taverna-activity-test-utils</artifactId> + <version>${taverna.engine.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>${project.parent.groupId}</groupId> + <artifactId>taverna-gis-client</artifactId> + <version>${project.parent.version}</version> + </dependency> + </dependencies> +</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java new file mode 100644 index 0000000..aa5c952 --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java @@ -0,0 +1,157 @@ +package org.apache.taverna.gis; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; + +import org.geotools.ows.ServiceException; +import org.n52.wps.client.ExecuteRequestBuilder; +import org.n52.wps.client.ExecuteResponseAnalyser; +import org.n52.wps.client.WPSClientException; +import org.n52.wps.client.WPSClientSession; +import org.n52.wps.io.data.IData; +import org.n52.wps.io.data.binding.complex.GTVectorDataBinding; + +import net.opengis.wps.x100.DataType; +import net.opengis.wps.x100.ExecuteDocument; +import net.opengis.wps.x100.ExecuteResponseDocument; +import net.opengis.wps.x100.OutputDataType; +import net.opengis.wps.x100.ProcessDescriptionType; +import org.apache.taverna.invocation.InvocationContext; +import org.apache.taverna.reference.ReferenceService; +import org.apache.taverna.reference.T2Reference; +import org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity; +import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException; +import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivity; +import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback; +import org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean; +import org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean; + +public class GisActivity extends AbstractAsynchronousActivity<GisActivityConfigurationBean> + implements AsynchronousActivity<GisActivityConfigurationBean> { + + private GisActivityConfigurationBean configBean; + + @Override + public void configure(GisActivityConfigurationBean configBean) throws ActivityConfigurationException { + + // TODO: Should I call HealthChecker here?? + // Any pre-config sanity checks + if (configBean.getOgcServiceUri().equals("")) { + throw new ActivityConfigurationException("Geospatial web service URI can't be empty"); + } + // Store for getConfiguration() + this.configBean = configBean; + + // REQUIRED: (Re)create input/output ports depending on configuration + configurePorts(); + } + + protected void configurePorts() { + // In case we are being reconfigured - remove existing ports first + // to avoid duplicates + removeInputs(); + removeOutputs(); + + // Add input ports + for(ActivityInputPortDefinitionBean inputPort : configBean.getInputPortDefinitions()) + { + addInput(inputPort.getName(),inputPort.getDepth(),inputPort.getAllowsLiteralValues(),inputPort.getHandledReferenceSchemes(), inputPort.getTranslatedElementType()); + } + + // Add output ports + for(ActivityOutputPortDefinitionBean outputPort : configBean.getOutputPortDefinitions()) + { + addOutput(outputPort.getName(),outputPort.getDepth()); + } + + } + + @SuppressWarnings("unchecked") + @Override + public void executeAsynch(final Map<String, T2Reference> inputs, final AsynchronousActivityCallback callback) { + // Execute service asynchronously + callback.requestRun(new Runnable() { + + public void run() { + InvocationContext context = callback.getContext(); + ReferenceService referenceService = context.getReferenceService(); + + // Declare outputs variable + Map<String, T2Reference> outputs = null; + + try { + + // prepare the execute object + WPSClientSession wpsClient = WPSClientSession.getInstance(); + + ProcessDescriptionType processDescription = wpsClient.getProcessDescription(configBean.getOgcServiceUri().toString(), configBean.getProcessIdentifier()); + + ExecuteRequestBuilder executeBuilder = new ExecuteRequestBuilder(processDescription); + + for (ActivityInputPortDefinitionBean activityInputPort : configBean.getInputPortDefinitions()) { + String portValue = (String) referenceService.renderIdentifier(inputs.get(activityInputPort.getName()), String.class, context); + executeBuilder.addLiteralData(activityInputPort.getName(), portValue); + } + + ExecuteDocument execute = executeBuilder.getExecute(); + + execute.getExecute().setService("WPS"); + + Object responseObject = null; + + try { + // execute service + responseObject = wpsClient.execute(configBean.getOgcServiceUri().toString(), execute); + } catch (WPSClientException e) { + // if the an error return from service + callback.fail(e.getServerException().xmlText()); + } + + // Register outputs + outputs = new HashMap<String, T2Reference>(); + T2Reference simpleRef = null; + + if (responseObject instanceof ExecuteResponseDocument) { + ExecuteResponseDocument response = (ExecuteResponseDocument) responseObject; + + // analyser is used to get complex data + ExecuteResponseAnalyser analyser = new ExecuteResponseAnalyser( + execute, response, processDescription); + + for(OutputDataType output : response.getExecuteResponse().getProcessOutputs().getOutputArray()) + { + DataType data = output.getData(); + + if (data.isSetLiteralData()) + { + simpleRef = referenceService.register(data.getLiteralData().getStringValue(), 0, true, context); + + outputs.put(output.getIdentifier().getStringValue(), simpleRef); + } + + } + + } + + + } catch (WPSClientException e) { + callback.fail(e.getMessage()); + } catch (IOException e) { + callback.fail(e.getMessage()); + } + + callback.receiveResult(outputs, new int[0]); + } + }); + } + + @Override + public GisActivityConfigurationBean getConfiguration() { + return this.configBean; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityConfigurationBean.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityConfigurationBean.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityConfigurationBean.java new file mode 100644 index 0000000..31d193b --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityConfigurationBean.java @@ -0,0 +1,52 @@ +package org.apache.taverna.gis; + +import java.io.Serializable; +import java.net.URI; +import java.util.List; + +import net.opengis.wps.x100.InputDescriptionType; +import net.opengis.wps.x100.OutputDescriptionType; +import org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean; + +/** + * Gis activity configuration bean. + * + */ +public class GisActivityConfigurationBean extends ActivityPortsDefinitionBean implements Serializable { + + /* + * TODO: Remove this comment. Should the jackson ojbect be managed in this class? + * + * The configuration specifies the variable options and configurations for + * an activity that has been added to a workflow. For instance for a WSDL + * activity, the configuration contains the URL for the WSDL together with + * the method name. String constant configurations contain the string that + * is to be returned, while Beanshell script configurations contain both the + * scripts and the input/output ports (by subclassing + * ActivityPortsDefinitionBean). + * + * Configuration beans are serialised as XML (currently by using XMLBeans) + * when Taverna is saving the workflow definitions. Therefore the + * configuration beans need to follow the JavaBeans style and only have + * fields of 'simple' types such as Strings, integers, etc. Other beans can + * be referenced as well, as long as they are part of the same plugin. + */ + + + private URI ogcServiceUri; + private String processIdentifier; + + public URI getOgcServiceUri() { + return ogcServiceUri; + } + public void setOgcServiceUri(URI ogcServiceUri) { + this.ogcServiceUri = ogcServiceUri; + } + public String getProcessIdentifier() { + return processIdentifier; + } + public void setProcessIdentifier(String processIdentifier) { + this.processIdentifier = processIdentifier; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityExample.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityExample.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityExample.java new file mode 100644 index 0000000..e533b43 --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityExample.java @@ -0,0 +1,132 @@ +package org.apache.taverna.gis; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import com.fasterxml.jackson.databind.JsonNode; + +import org.apache.taverna.invocation.InvocationContext; +import org.apache.taverna.reference.ReferenceService; +import org.apache.taverna.reference.T2Reference; +import org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity; +import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException; +import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivity; +import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback; + +/** + * Gis <code>Activity<code>. + */ +public class GisActivityExample extends AbstractAsynchronousActivity<JsonNode> + implements AsynchronousActivity<JsonNode> { + + public static final String ACTIVITY_TYPE = "http://example.com/2013/activity/apache-taverna-activity-gis";; + + /* + * Best practice: Keep port names as constants to avoid misspelling. This + * would not apply if port names are looked up dynamically from the service + * operation, like done for WSDL services. + */ + public static final String IN_FIRST_INPUT = "firstInput"; + public static final String IN_EXTRA_DATA = "extraData"; + public static final String OUT_MORE_OUTPUTS = "moreOutputs"; + public static final String OUT_SIMPLE_OUTPUT = "simpleOutput"; + public static final String OUT_REPORT = "report"; + + private JsonNode configuration; + + @Override + public void configure(JsonNode configuration) throws ActivityConfigurationException { + + // Any pre-config sanity checks + if (configuration.get("exampleString").asText().equals("invalidExample")) { + throw new ActivityConfigurationException( + "Example string can't be 'invalidExample'"); + } + // Store for getConfiguration(), but you could also make + // getConfiguration() return a new bean from other sources + this.configuration = configuration; + + // OPTIONAL: + // Do any server-side lookups and configuration, like resolving WSDLs + + // myClient = new MyClient(configuration.get("exampleUri").asText()); + // this.service = myClient.getService(configuration.get("exampleString").asText()); + + } + + @Override + public JsonNode getConfiguration() { + return configuration; + } + + @SuppressWarnings("unchecked") + @Override + public void executeAsynch(final Map<String, T2Reference> inputs, + final AsynchronousActivityCallback callback) { + // Don't execute service directly now, request to be run ask to be run + // from thread pool and return asynchronously + callback.requestRun(new Runnable() { + + public void run() { + InvocationContext context = callback + .getContext(); + ReferenceService referenceService = context + .getReferenceService(); + // Resolve inputs + String firstInput = (String) referenceService.renderIdentifier(inputs.get(IN_FIRST_INPUT), + String.class, context); + + // Support our configuration-dependendent input + boolean optionalPorts = configuration.get("exampleString").asText().equals("specialCase"); + + List<byte[]> special = null; + // We'll also allow IN_EXTRA_DATA to be optionally not provided + if (optionalPorts && inputs.containsKey(IN_EXTRA_DATA)) { + // Resolve as a list of byte[] + special = (List<byte[]>) referenceService.renderIdentifier( + inputs.get(IN_EXTRA_DATA), byte[].class, context); + } + + + // TODO: Do the actual service invocation +// try { +// results = this.service.invoke(firstInput, special) +// } catch (ServiceException ex) { +// callback.fail("Could not invoke Gis service " + configBean.getExampleUri(), +// ex); +// // Make sure we don't call callback.receiveResult later +// return; +// } + + // Register outputs + Map<String, T2Reference> outputs = new HashMap<>(); + String simpleValue = "simple"; + T2Reference simpleRef = referenceService.register(simpleValue, 0, true, context); + outputs.put(OUT_SIMPLE_OUTPUT, simpleRef); + + // For list outputs, only need to register the top level list + List<String> moreValues = new ArrayList<>(); + moreValues.add("Value 1"); + moreValues.add("Value 2"); + T2Reference moreRef = referenceService.register(moreValues, 1, true, context); + outputs.put(OUT_MORE_OUTPUTS, moreRef); + + if (optionalPorts) { + // Populate our optional output port + // NOTE: Need to return output values for all defined output ports + String report = "Everything OK"; + outputs.put(OUT_REPORT, referenceService.register(report, + 0, true, context)); + } + + // return map of output data, with empty index array as this is + // the only and final result (this index parameter is used if + // pipelining output) + callback.receiveResult(outputs, new int[0]); + } + }); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityFactory.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityFactory.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityFactory.java new file mode 100644 index 0000000..540dd3d --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityFactory.java @@ -0,0 +1,94 @@ +package org.apache.taverna.gis; + +import static org.apache.taverna.gis.GisActivity.*; + +import java.io.IOException; +import java.net.URI; +import java.util.HashSet; +import java.util.Set; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; + +import org.apache.taverna.workflowmodel.Edits; +import org.apache.taverna.workflowmodel.processor.activity.ActivityFactory; +import org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort; +import org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort; + +/** + * Gis <code>ActivityFactory<code>. + */ +public class GisActivityFactory implements ActivityFactory { + + private Edits edits; + + @Override + public GisActivity createActivity() { + return new GisActivity(); + } + + @Override + public URI getActivityType() { + return URI.create(GisActivity.ACTIVITY_TYPE); + } + + @Override + public JsonNode getActivityConfigurationSchema() { + ObjectMapper objectMapper = new ObjectMapper(); + try { + return objectMapper.readTree(getClass().getResource("/schema.json")); + } catch (IOException e) { + return objectMapper.createObjectNode(); + } + } + + @Override + public Set<ActivityInputPort> getInputPorts(JsonNode configuration) { + Set<ActivityInputPort> inputPorts = new HashSet<>(); + + // FIXME: Replace with your input port definitions + + // Hard coded input port, expecting a single String + inputPorts.add(edits.createActivityInputPort(IN_FIRST_INPUT, 0, true, null, String.class)); + + // Optional ports depending on configuration + if (configuration.get("exampleString").asText().equals("specialCase")) { + // depth 1, ie. list of binary byte[] arrays + inputPorts.add(edits.createActivityInputPort(IN_EXTRA_DATA, 1, true, null, byte[].class)); + } + + return inputPorts; + } + + @Override + public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration) { + Set<ActivityOutputPort> outputPorts = new HashSet<>(); + + // FIXME: Replace with your output port definitions + + // Optional ports depending on configuration + if (configuration.get("exampleString").asText().equals("specialCase")) { + outputPorts.add(edits.createActivityOutputPort(OUT_REPORT, 0, 0)); + } + + // Single value output port (depth 0) + outputPorts.add(edits.createActivityOutputPort(OUT_SIMPLE_OUTPUT, 0, 0)); + // Output port with list of values (depth 1) + outputPorts.add(edits.createActivityOutputPort(OUT_MORE_OUTPUTS, 1, 1)); + + return outputPorts; + } + + /** + * Sets the edits property. + * <p> + * This method is used by Spring. The property name must match the property specified + * in the Spring context file. + * + * @param edits the <code>Edits</code> used to create input/output ports + */ + public void setEdits(Edits edits) { + this.edits = edits; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityHealthChecker.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityHealthChecker.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityHealthChecker.java new file mode 100644 index 0000000..9e143b5 --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityHealthChecker.java @@ -0,0 +1,63 @@ +package org.apache.taverna.gis; + +import java.net.URI; +import java.util.ArrayList; +import java.util.List; + +import com.fasterxml.jackson.databind.JsonNode; + +import org.apache.taverna.visit.VisitReport; +import org.apache.taverna.visit.VisitReport.Status; +import org.apache.taverna.workflowmodel.health.HealthCheck; +import org.apache.taverna.workflowmodel.health.HealthChecker; + +/** + * Gis <code>HealthChecker</code>. + */ +public class GisActivityHealthChecker implements + HealthChecker<GisActivity> { + + public boolean canVisit(Object o) { + // Return True if we can visit the object. We could do + // deeper (but not time consuming) checks here, for instance + // if the health checker only deals with GisActivity where + // a certain configuration option is enabled. + return o instanceof GisActivity; + } + + public boolean isTimeConsuming() { + // Return true if the health checker does a network lookup + // or similar time consuming checks, in which case + // it would only be performed when using File->Validate workflow + // or File->Run. + return false; + } + + public VisitReport visit(GisActivity activity, List<Object> ancestry) { + JsonNode config = activity.getConfiguration(); + + // We'll build a list of subreports + List<VisitReport> subReports = new ArrayList<>(); + + if (!URI.create(config.get("exampleUri").asText()).isAbsolute()) { + // Report Severe problems we know won't work + VisitReport report = new VisitReport(HealthCheck.getInstance(), + activity, "Example URI must be absolute", HealthCheck.INVALID_URL, + Status.SEVERE); + subReports.add(report); + } + + if (config.get("exampleString").asText().equals("")) { + // Warning on possible problems + subReports.add(new VisitReport(HealthCheck.getInstance(), activity, + "Example string empty", HealthCheck.NO_CONFIGURATION, + Status.WARNING)); + } + + // The default explanation here will be used if the subreports list is + // empty + return new VisitReport(HealthCheck.getInstance(), activity, + "Gis service OK", HealthCheck.NO_PROBLEM, subReports); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/resources/schema.json ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/resources/schema.json b/apache-taverna-activity-gis-activity/src/main/resources/schema.json new file mode 100644 index 0000000..1e396b3 --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/resources/schema.json @@ -0,0 +1,25 @@ +{ + "$schema": "http://json-schema.org/draft-03/schema#";, + "id": "http://example.com/2013/activity/apache-taverna-activity-gis.schema.json";, + "title": "Gis activity configuration", + "type": "object", + "properties": { + "@context": { + "description": "JSON-LD context for interpreting the configuration as RDF", + "required": true, + "enum": ["http://example.com/2013/activity/apache-taverna-activity-gis.context.json";] + }, + "exampleString": { + "title": "Example String", + "description": "An example string property", + "type": "string", + "required": true + }, + "exampleUri": { + "title": "Example URI", + "description": "An example uri property", + "type": "string", + "required": true + } + } +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/resources/spring/context-osgi.xml ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/resources/spring/context-osgi.xml b/apache-taverna-activity-gis-activity/src/main/resources/spring/context-osgi.xml new file mode 100644 index 0000000..1b2a8c3 --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/resources/spring/context-osgi.xml @@ -0,0 +1,17 @@ +<?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";> + + <!-- Services to be registered with the OSGi service register --> + <service ref="GisActivityHealthChecker" interface="org.apache.taverna.workflowmodel.health.HealthChecker" /> + + <service ref="GisActivityFactory" interface="org.apache.taverna.workflowmodel.processor.activity.ActivityFactory" /> + + <!-- References to services required from the OSGi service register --> + <reference id="edits" interface="org.apache.taverna.workflowmodel.Edits" /> + +</beans:beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/resources/spring/context.xml ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/resources/spring/context.xml b/apache-taverna-activity-gis-activity/src/main/resources/spring/context.xml new file mode 100644 index 0000000..e2b290e --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/resources/spring/context.xml @@ -0,0 +1,12 @@ +<?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="GisActivityHealthChecker" class="org.apache.taverna.gis.GisActivityHealthChecker" /> + + <bean id="GisActivityFactory" class="org.apache.taverna.gis.GisActivityFactory"> + <property name="edits" ref="edits" /> + </bean> + +</beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/main/resources/wps_config.xml ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/main/resources/wps_config.xml b/apache-taverna-activity-gis-activity/src/main/resources/wps_config.xml new file mode 100644 index 0000000..cd73904 --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/main/resources/wps_config.xml @@ -0,0 +1,212 @@ +<?xml version="1.0" encoding="UTF-8"?> +<WPSConfiguration xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; + xsi:schemaLocation="http://n52.org/wps https://raw.githubusercontent.com/52North/wps-config/52n-wps-config-1.2.1/src/main/xsd/schema_v2.xsd"; xmlns="http://n52.org/wps";> + <Datahandlers> + <ParserList> + <Parser name="WCPSQueryParser" + className="org.n52.wps.io.datahandler.parser.WCPSQueryParser" + active="true"> + <Format mimetype="text/plain" + schema="http://schemas.opengis.net/wcps/1.0/wcpsAll.xsd"; /> + </Parser> + <Parser name="WKTParser" + className="org.n52.wps.io.datahandler.parser.WKTParser" + active="true"> + <Format mimetype="application/wkt"/> + </Parser> + <Parser name="GenericXMLDataParser" + className="org.n52.wps.io.datahandler.parser.GenericXMLDataParser" + active="true"> + <Format mimetype="text/xml" /> + <Format mimetype="text/xml; subtype=gml/2.1.2" + schema="http://schemas.opengis.net/gml/2.1.2/feature.xsd"; /> + </Parser> + <Parser name="GenericFileParser" + className="org.n52.wps.io.datahandler.parser.GenericFileParser" + active="true"> + <Format mimetype="application/x-zipped-shp" /> + <Format mimetype="application/img" /> + <Format mimetype="image/tiff" /> + <Format mimetype="image/geotiff" /> + <Format mimetype="application/geotiff" /> + <Format mimetype="application/dbase" /> + <Format mimetype="application/remap" /> + <Format mimetype="application/x-erdas-hfa" /> + <Format mimetype="application/x-netcdf" /> + <Format mimetype="application/dgn" /> + <Format mimetype="image/jpeg" /> + <Format mimetype="image/png" /> + <Format mimetype="application/x-geotiff" /> + <Format mimetype="application/hdf4-eos" /> + <Format mimetype="text/plain" /> + <Format mimetype="application/rData" /> + <Format mimetype="application/rData+Spatial" /> + <Format mimetype="application/rData+SpatialPoints" /> + <Format mimetype="application/rData+SpatialPolygons" /> + <Format mimetype="text/html" /> + + <Format mimetype="application/rData" encoding="base64" /> + <Format mimetype="application/rData+Spatial" encoding="base64" /> + <Format mimetype="application/rData+SpatialPoints" encoding="base64" /> + <Format mimetype="application/rData+SpatialPolygons" encoding="base64" /> + <Format mimetype="application/x-zipped-shp" encoding="base64" /> + <Format mimetype="application/img" encoding="base64" /> + <Format mimetype="image/tiff" encoding="base64" /> + <Format mimetype="application/geotiff" encoding="base64" /> + <Format mimetype="application/dbase" encoding="base64" /> + <Format mimetype="application/remap" encoding="base64" /> + <Format mimetype="application/x-erdas-hfa" encoding="base64" /> + <Format mimetype="application/x-netcdf" encoding="base64" /> + <Format mimetype="application/dgn" encoding="base64" /> + <Format mimetype="image/jpeg" encoding="base64" /> + <Format mimetype="image/png" encoding="base64" /> + <Format mimetype="application/x-geotiff" encoding="base64" /> + <Format mimetype="application/hdf4-eos" encoding="base64" /> + <Format mimetype="text/plain" encoding="base64" /> + </Parser> + </ParserList> + <GeneratorList> + <Generator name="WKTGenerator" + className="org.n52.wps.io.datahandler.generator.WKTGenerator" + active="true"> + <Format mimetype="application/wkt"/> + </Generator> + <Generator name="GenericXMLDataGenerator" + className="org.n52.wps.io.datahandler.generator.GenericXMLDataGenerator" + active="true"> + <Format mimetype="text/xml" /> + <Format mimetype="text/xml; subtype=gml/2.1.2" + schema="http://schemas.opengis.net/gml/2.1.2/feature.xsd"; /> + </Generator> + <Generator name="GenericFileGenerator" + className="org.n52.wps.io.datahandler.generator.GenericFileGenerator" + active="true"> + <Format mimetype="application/x-zipped-shp" encoding="base64" /> + <Format mimetype="application/shp" encoding="base64" /> + <Format mimetype="application/img" encoding="base64" /> + <Format mimetype="image/tiff" encoding="base64" /> + <Format mimetype="image/geotiff" encoding="base64" /> + <Format mimetype="application/geotiff" encoding="base64" /> + <Format mimetype="application/dbase" encoding="base64" /> + <Format mimetype="application/remap" encoding="base64" /> + <Format mimetype="application/x-erdas-hfa" encoding="base64" /> + <Format mimetype="application/x-netcdf" encoding="base64" /> + <Format mimetype="application/netcdf" encoding="base64" /> + <Format mimetype="application/dgn" encoding="base64" /> + <Format mimetype="image/jpeg" encoding="base64" /> + <Format mimetype="image/png" encoding="base64" /> + <Format mimetype="application/x-geotiff" encoding="base64" /> + <Format mimetype="text/plain" encoding="base64" /> + <Format mimetype="application/x-zipped-shp" encoding="base64" /> + <Format mimetype="application/rData" encoding="base64" /> + <Format mimetype="application/rData+Spatial" encoding="base64" /> + <Format mimetype="application/rData+SpatialPoints" encoding="base64" /> + <Format mimetype="application/rData+SpatialPolygons" encoding="base64" /> + + <Format mimetype="application/rData" /> + <Format mimetype="application/rData+Spatial" /> + <Format mimetype="application/rData+SpatialPoints" /> + <Format mimetype="application/rData+SpatialPolygons" /> + <Format mimetype="application/x-zipped-shp" /> + <Format mimetype="application/shp" /> + <Format mimetype="application/img" /> + <Format mimetype="image/tiff" /> + <Format mimetype="image/geotiff" /> + <Format mimetype="application/geotiff" /> + <Format mimetype="application/dbase" /> + <Format mimetype="application/remap" /> + <Format mimetype="application/x-erdas-hfa" /> + <Format mimetype="application/x-netcdf" /> + <Format mimetype="application/netcdf" /> + <Format mimetype="application/dgn" /> + <Format mimetype="image/jpeg" /> + <Format mimetype="image/png" /> + <Format mimetype="application/x-geotiff" /> + <Format mimetype="text/plain" /> + <Format mimetype="application/pdf" /> + <Format mimetype="application/zip" /> + <Format mimetype="text/html" /> + </Generator> + </GeneratorList> + </Datahandlers> + <AlgorithmRepositoryList> + <Repository name="LocalAlgorithmRepository" + className="org.n52.wps.server.LocalAlgorithmRepository" active="true"> + <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.JTSConvexHullAlgorithm</Property> + <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.DummyTestClass</Property> + <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.LongRunningDummyTestClass</Property> + <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.MultipleComplexInAndOutputsDummyTestClass</Property> + <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.MultiReferenceInputAlgorithm</Property> + <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.MultiReferenceBinaryInputAlgorithm</Property> + <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.EchoProcess</Property> + </Repository> + <Repository name="UploadedAlgorithmRepository" + className="org.n52.wps.server.UploadedAlgorithmRepository" active="false"> + </Repository> + <Repository name="ServiceLoaderAlgorithmRepository" + className="org.n52.wps.server.ServiceLoaderAlgorithmRepository" active="true"> + </Repository> + <!-- + <Repository name="MCProcessRepository" className="org.n52.wps.mc.MCProcessRepository" active="true"> + <Property name="REMOTE_REPOSITORY" active="false">http://141.30.100.178/gpfeed2/gpfeed.xml</Property> + <Property name="LOCAL_REPOSITORY" active="true">D:\MCpackages</Property> + </Repository> + --> + </AlgorithmRepositoryList> + <RemoteRepositoryList /> + + <Server protocol="http" hostname="localhost" hostport="8080" + includeDataInputsInResponse="false" computationTimeoutMilliSeconds="5" + cacheCapabilites="false" webappPath="wps" repoReloadInterval="0" maxPoolSize="20" keepAliveSeconds="1000" maxQueuedTasks="100" minPoolSize="10" > + <!-- Setting to 'true' will enable filtering of responses documents. Any server URL in + the response document will be replaced with the server URL used in the HTTP request. --> + <Property name="responseURLFilterEnabled" active="true">false</Property> + <Database> + <!-- NOTE: database wipe is only implemented for the FlatFileDatabase (the default) --> + <!-- enable database wiping base on values below --> + <Property name="wipe.enabled" active="true">true</Property> + <!-- scans database every 1 hour --> + <Property name="wipe.period" active="true">PT1H</Property> + <!-- deletes files older than 7 days --> + <Property name="wipe.threshold" active="true">P7D</Property> + </Database> + + <!-- + POSTGRES Connector + ================== + Ensure that the postgres driver is available to the server during + launch. The server will fail to start if Postgres is active but the + driver is missing. However, if the driver exists and the database + cannot be connected to (unavailable, username/pass issue, etc), the + framework will fail-over to the Flatfile Database + jndiName or username/password: If jndiName exists, username + and password are not used. + saveResultsToDb: Setting to false will save results output to file + and put the URI link to the file in the database. Setting to true + stores the actual result output in the database (You probably don't + want this if you have large results). + JNDI Configuration: + <Database> + <Property active="true" name="databaseClass">org.n52.wps.server.database.PostgresDatabase</Property> + <Property active="true" name="jndiName">jndiname</Property> + <Property active="true" name="saveResultsToDb">false</Property> + <Property name="wipe.enabled" active="true">true</Property> + <Property name="wipe.period" active="true">PT1H</Property> + <Property name="wipe.threshold" active="true">P7D</Property> + </Database> + Direct connection configuration: + <Database> + Alternative connection method + <Property active="true" name="databaseName">postgres</Property> + <Property active="true" name="databasePath">//localhost:5432</Property> + <Property active="true" name="username">username</Property> + <Property active="true" name="password">password</Property> + <Property active="true" name="saveResultsToDb">false</Property> + <Property name="wipe.enabled" active="true">true</Property> + <Property name="wipe.period" active="true">PT1H</Property> + <Property name="wipe.threshold" active="true">P7D</Property> + </Database> +--> + + </Server> +</WPSConfiguration> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityFactoryTest.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityFactoryTest.java b/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityFactoryTest.java new file mode 100644 index 0000000..4b137c6 --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityFactoryTest.java @@ -0,0 +1,100 @@ +package org.apache.taverna.gis; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertNotSame; +import static org.junit.Assert.assertTrue; + +import java.net.URI; +import java.util.HashSet; +import java.util.Set; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.node.JsonNodeFactory; +import com.fasterxml.jackson.databind.node.ObjectNode; + +import org.apache.taverna.workflowmodel.impl.EditsImpl; +import org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort; +import org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort; + +import org.junit.Before; +import org.junit.Test; + +public class GisActivityFactoryTest { + + private ObjectNode configuration; + + private GisActivityFactory activityFactory; + + @Before + public void setUp() throws Exception { + configuration = JsonNodeFactory.instance.objectNode(); + configuration.put("exampleString", "something"); + configuration.put("exampleUri", "http://localhost:8080/myEndPoint";); + + activityFactory = new GisActivityFactory(); + activityFactory.setEdits(new EditsImpl()); + } + + @Test + public void testCreateActivity() { + GisActivity activity = activityFactory.createActivity(); + assertNotNull(activity); + assertNotSame(activity, activityFactory.createActivity()); + } + + @Test + public void testGetActivityURI() { + assertEquals(URI.create(GisActivity.ACTIVITY_TYPE), activityFactory.getActivityType()); + } + + @Test + public void testGetActivityConfigurationSchema() { + JsonNode configurationSchema = activityFactory.getActivityConfigurationSchema(); + assertNotNull(configurationSchema); + assertTrue(configurationSchema.has("properties")); + JsonNode propertiesNode = configurationSchema.get("properties"); + assertTrue(propertiesNode.has("exampleString")); + assertTrue(propertiesNode.has("exampleUri")); + } + + @Test + public void testGetInputPorts() { + Set<String> expectedInputs = new HashSet<String>(); + expectedInputs.add("firstInput"); + + Set<ActivityInputPort> inputPorts = activityFactory.getInputPorts(configuration); + assertEquals("Unexpected inputs", expectedInputs.size(), inputPorts.size()); + for (ActivityInputPort inputPort : inputPorts) { + assertTrue("Wrong input : " + inputPort.getName(), expectedInputs + .remove(inputPort.getName())); + } + + ObjectNode specialConfiguration = JsonNodeFactory.instance.objectNode(); + specialConfiguration.put("exampleString", "specialCase"); + specialConfiguration.put("exampleUri", "http://localhost:8080/myEndPoint";); + + assertEquals("Unexpected inputs", 2, activityFactory.getInputPorts(specialConfiguration).size()); + } + + @Test + public void testGetOutputPorts() { + Set<String> expectedOutputs = new HashSet<String>(); + expectedOutputs.add("simpleOutput"); + expectedOutputs.add("moreOutputs"); + + Set<ActivityOutputPort> outputPorts = activityFactory.getOutputPorts(configuration); + assertEquals("Unexpected outputs", expectedOutputs.size(), outputPorts.size()); + for (ActivityOutputPort outputPort : outputPorts) { + assertTrue("Wrong output : " + outputPort.getName(), + expectedOutputs.remove(outputPort.getName())); + } + + ObjectNode specialConfiguration = JsonNodeFactory.instance.objectNode(); + specialConfiguration.put("exampleString", "specialCase"); + specialConfiguration.put("exampleUri", "http://localhost:8080/myEndPoint";); + + assertEquals("Unexpected outputs", 3, activityFactory.getOutputPorts(specialConfiguration).size()); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityTest.java ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityTest.java b/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityTest.java new file mode 100644 index 0000000..1134774 --- /dev/null +++ b/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityTest.java @@ -0,0 +1,73 @@ +package org.apache.taverna.gis; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +import java.net.URI; +import java.util.Arrays; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.node.JsonNodeFactory; +import com.fasterxml.jackson.databind.node.ObjectNode; + +import org.apache.taverna.activities.testutils.ActivityInvoker; +import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException; +import org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort; +import org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort; + +import org.junit.Before; +import org.junit.Test; + +public class GisActivityTest { + + private ObjectNode configuration; + + private GisActivity activity = new GisActivity(); + + @Before + public void makeConfiguration() throws Exception { + configuration = JsonNodeFactory.instance.objectNode(); + configuration.put("exampleString", "something"); + configuration.put("exampleUri", "http://localhost:8080/myEndPoint";); + } + + @Test + public void configureActivity() throws Exception { + activity.configure(configuration); + assertTrue(configuration.equals(activity.getConfiguration())); + } + + @Test(expected = ActivityConfigurationException.class) + public void invalidConfiguration() throws ActivityConfigurationException { + ObjectNode invalidBean = JsonNodeFactory.instance.objectNode(); + invalidBean.put("exampleString", "invalidExample"); + // Should throw ActivityConfigurationException + activity.configure(invalidBean); + } + + @Test + public void executeAsynch() throws Exception { + activity.configure(configuration); + + Map<String, Object> inputs = new HashMap<String, Object>(); + inputs.put("firstInput", "hello"); + + Map<String, Class<?>> expectedOutputTypes = new HashMap<String, Class<?>>(); + expectedOutputTypes.put("simpleOutput", String.class); + expectedOutputTypes.put("moreOutputs", String.class); + + Map<String, Object> outputs = ActivityInvoker.invokeAsyncActivity( + activity, inputs, expectedOutputTypes); + + assertEquals("Unexpected outputs", 2, outputs.size()); + assertEquals("simple", outputs.get("simpleOutput")); + assertEquals(Arrays.asList("Value 1", "Value 2"), outputs + .get("moreOutputs")); + + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/3ca3856a/apache-taverna-activity-gis-plugin/pom.xml ---------------------------------------------------------------------- diff --git a/apache-taverna-activity-gis-plugin/pom.xml b/apache-taverna-activity-gis-plugin/pom.xml new file mode 100644 index 0000000..ebc2cd5 --- /dev/null +++ b/apache-taverna-activity-gis-plugin/pom.xml @@ -0,0 +1,28 @@ +<?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>org.apache.taverna.gis</groupId> + <artifactId>apache-taverna-activity-gis</artifactId> + <version>0.0.1-incubating.SNAPSHOT</version> + </parent> + <artifactId>apache-taverna-activity-gis-plugin</artifactId> + <packaging>taverna-plugin</packaging> + <name>Gis Taverna plugin</name> + <description>Description of Example Taverna plugin</description> + <dependencies> + <dependency> + <groupId>${project.groupId}</groupId> + <artifactId>apache-taverna-activity-gis-activity</artifactId> + <version>0.0.1-incubating.SNAPSHOT</version> + </dependency> + <!-- Enable for Workbench integration + <dependency> + <groupId>${project.groupId}</groupId> + <artifactId>apache-taverna-activity-gis-activity-ui</artifactId> + <version>0.0.1-incubating.SNAPSHOT</version> + </dependency> + --> + </dependencies> +</project>
