* * @author Martin Senger * @version $Id: Taverna.java,v 1.4 2005/07/19 12:39:59 senger Exp $ */ public abstract class Taverna { /** Property name. A boolean value. If set to true the generated * workflow definition does not include input data processor * (converting basic data types into Moby XML structure). Default * is false. */ public static final String PROP_RAWINPUT = "rawinput"; /** Property name. A boolean value. If set to true the generated * workflow definition does not include output data * processor (converting basic data types from Moby XML * structure). Default is false. */ public static final String PROP_RAWOUTPUT = "rawoutput"; /** Property name. A boolean value. If set to true workflow * creation produces many Taverna messages. Default is false. */ public static final String PROP_VERBOSE = "tverbose"; /************************************************************************* * Creates a workflow definition (an XML string known as 'scufl' * or 'xscufl') from the set of graph edges. The definition * includes also pointer to a BioMoby registry where the services * (used by graph edges) are registered.
* * @param edges represent services and their connectors in the * created graph; some edges may be of type {@link * DataServiceEdge} (which is a subclass of ServicesEdge) - those * represent a special type of connection between a service and an * input or ouput data type; the graph represented by these edges * should not have cycles and should not have forking and merging * branches * * @param props are some properties that can influence how the * workflow definition will look like; see the property names * elsewhere in this API what properties are understood * * @return a string with a scufl workflow definition *************************************************************************/ public static String buildWorkflow (ServicesEdge[] edges, String mobyEndpoint, Properties props) throws MobyException { try { // properties influencing workflow definition boolean verbose = ( props.containsKey (PROP_VERBOSE) && props.getProperty (PROP_VERBOSE).equals ("true") ); boolean rawinput = ( props.containsKey (PROP_RAWINPUT) && props.getProperty (PROP_RAWINPUT).equals ("true") ); boolean rawoutput = ( props.containsKey (PROP_RAWOUTPUT) && props.getProperty (PROP_RAWOUTPUT).equals ("true") ); ScuflModel model = new ScuflModel(); model.setOffline (true); model.isFiringEvents = verbose; Hashtable processors = new Hashtable(); for (int i = 0; i < edges.length; i++) { if (edges[i] instanceof DataServiceEdge) { DataServiceEdge edge = (DataServiceEdge)edges[i]; if (edge.isEndingEdge()) { // add a (potentially new) BioMoby processor (representing a source service) String sourceName = addMobyProcessor (model, edge.getSourceService(), mobyEndpoint, processors); // add a sink for result String sinkName; if (rawoutput) { sinkName = model.getValidProcessorName (edge.getConnector()); Processor sinkProcessor = model.getWorkflowSinkProcessor(); InputPort sinkPort = new InputPort (sinkProcessor, sinkName); sinkPort.getMetadata().setDescription (edge.getDataType().getDescription()); sinkProcessor.addPort (sinkPort); } else { // create a local processor that extract // from XML/Moby formatted output data into // several output pieces (namespace, id [, value]) String mobyOutputName = model.getValidProcessorName ("MobyOutput"); String mobyPort = "mobydata"; sinkName = mobyOutputName + ":" + mobyPort; Processor extractMobyDataProcessor = new LocalServiceProcessor (model, mobyOutputName, "org.embl.ebi.escience.scuflworkers.biomoby.ExtractMobyData"); extractMobyDataProcessor.setDescription (edge.getDataType().getDescription()); model.addProcessor (extractMobyDataProcessor); // create output boxes (for namespace, id, // type, value) Processor sinkProcessor = model.getWorkflowSinkProcessor(); String namespaceName = model.getValidProcessorName ("namespace"); sinkProcessor.addPort (new InputPort (sinkProcessor, namespaceName)); model.addDataConstraint (new DataConstraint (model, mobyOutputName + ":namespace", namespaceName)); String idName = model.getValidProcessorName ("id"); sinkProcessor.addPort (new InputPort (sinkProcessor, idName)); model.addDataConstraint (new DataConstraint (model, mobyOutputName + ":id", idName)); String typeName = model.getValidProcessorName ("type"); sinkProcessor.addPort (new InputPort (sinkProcessor, typeName)); model.addDataConstraint (new DataConstraint (model, mobyOutputName + ":type", typeName)); String valueName = model.getValidProcessorName ("value"); sinkProcessor.addPort (new InputPort (sinkProcessor, valueName)); model.addDataConstraint (new DataConstraint (model, mobyOutputName + ":value", valueName)); } // connect them together DataConstraint dc = new DataConstraint (model, sourceName + ":output", sinkName); model.addDataConstraint (dc); } else { // add a (potentially new) BioMoby processor (representing a target service) String targetName = addMobyProcessor (model, edge.getTargetService(), mobyEndpoint, processors); // add a source for workflow main input String inputName; if (rawinput) { inputName = model.getValidProcessorName (edge.getConnector()); Processor sourceProcessor = model.getWorkflowSourceProcessor(); OutputPort sourcePort = new OutputPort (sourceProcessor, inputName); sourcePort.getMetadata().setDescription (edge.getDataType().getDescription()); sourceProcessor.addPort (sourcePort); } else { // create a local processor that creates // Moby input data in XML/Moby format from // several input pieces (namespace, id [, value]) String mobyInputName = model.getValidProcessorName ("MobyInput"); String mobyPort = "mobydata"; inputName = mobyInputName + ":" + mobyPort; Processor createMobyDataProcessor = new LocalServiceProcessor (model, mobyInputName, "org.embl.ebi.escience.scuflworkers.biomoby.CreateMobyData"); createMobyDataProcessor.setDescription (edge.getDataType().getDescription()); model.addProcessor (createMobyDataProcessor); // create input boxes: Processor sourceProcessor = model.getWorkflowSourceProcessor(); // a) always for namespace, id String ns = edge.extractNamespace(); String namespaceName = model.getValidProcessorName ("namespace"); if (ns.equals ("")) { sourceProcessor.addPort (new OutputPort (sourceProcessor, namespaceName)); model.addDataConstraint (new DataConstraint (model, namespaceName, mobyInputName + ":namespace")); } else { // when we know a Moby namespace of this input, make it a string constant String procName = model.getValidProcessorName (ns); Processor stringProcessor = new StringConstantProcessor (model, procName, ns); stringProcessor.addPort (new OutputPort (sourceProcessor, ns)); model.addProcessor (stringProcessor); model.addDataConstraint (new DataConstraint (model, procName + ":value", mobyInputName + ":namespace")); } String idName = model.getValidProcessorName ("id"); sourceProcessor.addPort (new OutputPort (sourceProcessor, idName)); model.addDataConstraint (new DataConstraint (model, idName, mobyInputName + ":id")); // b) for basic types (if the input is a basic type) String valueName = model.getValidProcessorName ("value"); String dt = Utils.pureName (edge.getDataType().getName()); if (dt.equalsIgnoreCase ("String")) { sourceProcessor.addPort (new OutputPort (sourceProcessor, valueName)); model.addDataConstraint (new DataConstraint (model, valueName, mobyInputName + ":stringvalue")); } else if (dt.equalsIgnoreCase ("Integer")) { sourceProcessor.addPort (new OutputPort (sourceProcessor, valueName)); model.addDataConstraint (new DataConstraint (model, valueName, mobyInputName + ":intvalue")); } else if (dt.equalsIgnoreCase ("Float")) { sourceProcessor.addPort (new OutputPort (sourceProcessor, valueName)); model.addDataConstraint (new DataConstraint (model, valueName, mobyInputName + ":floatvalue")); // } else if (! dt.equalsIgnoreCase ("Object")) { // sourceProcessor.addPort (new OutputPort (sourceProcessor, valueName)); // model.addDataConstraint (new DataConstraint (model, valueName, mobyInputName + ":payload")); } } // connect them together DataConstraint dc = new DataConstraint (model, inputName, targetName + ":input"); model.addDataConstraint (dc); } } else { ServicesEdge edge = edges[i]; // add a new BioMoby processor (representing a source service) String sourceName = addMobyProcessor (model, edge.getSourceService(), mobyEndpoint, processors); // add a new BioMoby processor (representing a target service) String targetName = addMobyProcessor (model, edge.getTargetService(), mobyEndpoint, processors); // connect these two nodes/services/processors DataConstraint dc = new DataConstraint (model, sourceName + ":output", targetName + ":input"); model.addDataConstraint (dc); } } // XScuflParser.java for more details. XScuflView xsv = new XScuflView (model); return xsv.getXMLText(); } catch (MobyException e) { throw (e); } catch (Exception e) { e.printStackTrace(); throw new MobyException (e.toString()); } } // returns a name of the new (or existing) processor static String addMobyProcessor (ScuflModel model, MobyService service, String mobyEndpoint, Hashtable processorsSoFar) throws MobyException { try { String serviceId = service.getUniqueName(); if (processorsSoFar.containsKey (serviceId)) return (String)processorsSoFar.get (serviceId); String processorName = model.getValidProcessorName (service.getName()); BiomobyProcessor mobyProcessor = new BiomobyProcessor (model, processorName, service, mobyEndpoint); String description = service.getDescription(); if (description != null) mobyProcessor.setDescription (description); model.addProcessor (mobyProcessor); processorsSoFar.put (serviceId, processorName); return processorName; } catch (Exception e) { throw new MobyException (e.toString()); } } // StringConstantProcessor }