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@@ -1,1553 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- * 
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.soap;
-
-import static org.taverna.server.master.common.Namespaces.SERVER_SOAP;
-import static org.taverna.server.master.common.Roles.USER;
-
-import java.net.URI;
-import java.util.Date;
-import java.util.List;
-
-import javax.annotation.security.RolesAllowed;
-import javax.jws.WebMethod;
-import javax.jws.WebParam;
-import javax.jws.WebResult;
-import javax.jws.WebService;
-import javax.xml.bind.annotation.XmlElement;
-
-import org.apache.cxf.annotations.WSDLDocumentation;
-import org.ogf.usage.JobUsageRecord;
-import org.taverna.server.master.common.Capability;
-import org.taverna.server.master.common.Credential;
-import org.taverna.server.master.common.DirEntryReference;
-import org.taverna.server.master.common.InputDescription;
-import org.taverna.server.master.common.Permission;
-import org.taverna.server.master.common.ProfileList;
-import org.taverna.server.master.common.RunReference;
-import org.taverna.server.master.common.Status;
-import org.taverna.server.master.common.Trust;
-import org.taverna.server.master.common.Workflow;
-import org.taverna.server.master.common.version.Version;
-import org.taverna.server.master.exceptions.BadPropertyValueException;
-import org.taverna.server.master.exceptions.BadStateChangeException;
-import org.taverna.server.master.exceptions.FilesystemAccessException;
-import org.taverna.server.master.exceptions.InvalidCredentialException;
-import org.taverna.server.master.exceptions.NoCreateException;
-import org.taverna.server.master.exceptions.NoCredentialException;
-import org.taverna.server.master.exceptions.NoDirectoryEntryException;
-import org.taverna.server.master.exceptions.NoListenerException;
-import org.taverna.server.master.exceptions.NoUpdateException;
-import org.taverna.server.master.exceptions.NotOwnerException;
-import org.taverna.server.master.exceptions.UnknownRunException;
-import org.taverna.server.master.rest.TavernaServerREST;
-import org.taverna.server.port_description.OutputDescription;
-
-/**
- * The SOAP service interface to Taverna 3 Server.
- * 
- * @author Donal Fellows
- * @see TavernaServerREST
- */
-@RolesAllowed(USER)
-@WebService(name = "tavernaService", targetNamespace = SERVER_SOAP)
-@WSDLDocumentation("The SOAP service interface to Taverna " + Version.JAVA
-               + " Server.")
-public interface TavernaServerSOAP {
-       /**
-        * Make a run for a particular workflow.
-        * 
-        * @param workflow
-        *            The workflow to instantiate.
-        * @return Annotated handle for created run.
-        * @throws NoUpdateException
-        * @throws NoCreateException
-        */
-       @WebResult(name = "Run")
-       @WSDLDocumentation("Make a run for a particular workflow.")
-       RunReference submitWorkflow(
-                       @WebParam(name = "workflow") @XmlElement(required = 
true) Workflow workflow)
-                                       throws NoUpdateException, 
NoCreateException;
-
-       /**
-        * Make a run for a particular workflow.
-        * 
-        * @param workflow
-        *            The workflow to instantiate.
-        * @return Annotated handle for created run.
-        * @throws NoUpdateException
-        * @throws NoCreateException
-        */
-       @WebResult(name = "Run")
-       @WSDLDocumentation("Make a run for a particular workflow.")
-       RunReference submitWorkflowMTOM(
-                       @WebParam(name = "workflow") @XmlElement(required = 
true) WrappedWorkflow workflow)
-                       throws NoUpdateException;
-
-       /**
-        * Make a run for a particular workflow, where that workflow will be
-        * downloaded from elsewhere. The URI <i>must</i> be publicly readable.
-        * 
-        * @param workflowURI
-        *            The URI to the workflow to instantiate.
-        * @return Annotated handle for created run.
-        * @throws NoUpdateException
-        * @throws NoCreateException
-        */
-       @WebResult(name = "Run")
-       @WSDLDocumentation("Make a run for a particular workflow where that "
-                       + "workflow is given by publicly readable URI.")
-       RunReference submitWorkflowByURI(
-                       @WebParam(name = "workflowURI") @XmlElement(required = 
true) URI workflowURI)
-                       throws NoCreateException, NoUpdateException;
-
-       /**
-        * Get the list of existing runs owned by the user.
-        * 
-        * @return Annotated handle list.
-        */
-       @WebResult(name = "Run")
-       @WSDLDocumentation("Get the list of existing runs owned by the user.")
-       RunReference[] listRuns();
-
-       /**
-        * Get the upper limit on the number of runs that the user may create at
-        * once.
-        * 
-        * @return The limit. <b>NB:</b> the number currently operating may be
-        *         larger, but in that case no further runs can be made until 
some
-        *         of the old ones are destroyed.
-        */
-       @WebResult(name = "MaxSimultaneousRuns")
-       @WSDLDocumentation("Get the upper limit on the number of runs that the 
user may create at once.")
-       int getServerMaxRuns();
-
-       /**
-        * Get the list of allowed workflows. If the list is empty, <i>any</i>
-        * workflow may be used.
-        * 
-        * @return A list of workflow documents.
-        */
-       @WebMethod(operationName = "getPermittedWorkflowURIs")
-       @WebResult(name = "PermittedWorkflowURI")
-       @WSDLDocumentation("Get the list of URIs to allowed workflows. If the 
list is empty, any workflow may be used including those not submitted via URI.")
-       URI[] getServerWorkflows();
-
-       /**
-        * Get the list of allowed event listeners.
-        * 
-        * @return A list of listener names.
-        */
-       @WebMethod(operationName = "getPermittedListenerTypes")
-       @WebResult(name = "PermittedListenerType")
-       @WSDLDocumentation("Get the list of allowed types of event listeners.")
-       String[] getServerListeners();
-
-       /**
-        * Get the list of notification fabrics.
-        * 
-        * @return A list of listener names.
-        */
-       @WebMethod(operationName = "getEnabledNotificationFabrics")
-       @WebResult(name = "EnabledNotifierFabric")
-       @WSDLDocumentation("Get the list of notification fabrics. Each is a URI 
scheme.")
-       String[] getServerNotifiers();
-
-       @WebMethod(operationName = "getCapabilities")
-       @WebResult(name = "Capabilities")
-       @WSDLDocumentation("Get the workflow execution capabilities of this "
-                       + "Taverna Server instance.")
-       List<Capability> getServerCapabilities();
-
-       /**
-        * Destroy a run immediately. This might or might not actually 
relinquish
-        * resources; that's up to the service implementation and deployment.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the lifetime of 
the
-        *             run.
-        */
-       @WSDLDocumentation("Destroy a run immediately.")
-       void destroyRun(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException, NoUpdateException;
-
-       /**
-        * Get the workflow document used to create the given run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The workflow document.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "CreationWorkflow")
-       @WSDLDocumentation("Get the workflow document used to create the given 
run.")
-       Workflow getRunWorkflow(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Get the workflow document used to create the given run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The workflow document.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "CreationWorkflow")
-       @WSDLDocumentation("Get the workflow document used to create the given 
run.")
-       WrappedWorkflow getRunWorkflowMTOM(
-                       @WebParam(name = "runName") String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Get a description of the profiles supported by the workflow document 
used
-        * to create the given run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return A description of the supported profiles.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "Profiles")
-       @WSDLDocumentation("Get a description of the profiles supported by the 
workflow document used to create the given run.")
-       ProfileList getRunWorkflowProfiles(
-                       @WebParam(name = "runName") String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Get the descriptive name of the workflow run. The descriptive name
-        * carries no deep information.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The descriptive name of the run.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "DescriptiveName")
-       @WSDLDocumentation("Get the descriptive name of the workflow run. 
Carries no deep information.")
-       String getRunDescriptiveName(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Set the descriptive name of the workflow run. The descriptive name
-        * carries no deep information.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param descriptiveName
-        *            The new descriptive name to set. Note that the 
implementation
-        *            is allowed to arbitrarily truncate this value.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user is not permitted to update this run.
-        */
-       @WSDLDocumentation("Set the descriptive name of the workflow run. 
Carries no deep information.")
-       void setRunDescriptiveName(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "descriptiveName") 
@XmlElement(required = true) String descriptiveName)
-                       throws UnknownRunException, NoUpdateException;
-
-       /**
-        * Get the description of the inputs to the workflow run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The input description
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "RunInputDescription")
-       @WSDLDocumentation("Get the description of the inputs currently set up 
for the given workflow run.")
-       InputDescription getRunInputs(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Get a description of what inputs the workflow run <i>expects</i> to
-        * receive.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The description document.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "RunInputDescriptor")
-       @WSDLDocumentation("Get a description of what inputs the given workflow 
run expects to receive.")
-       org.taverna.server.port_description.InputDescription 
getRunInputDescriptor(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Tells the run to use the given Baclava file for all inputs.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param fileName
-        *            The name of the file to use. Must not start with a 
<tt>/</tt>
-        *            or contain a <tt>..</tt> element.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the run.
-        * @throws FilesystemAccessException
-        *             If the filename is illegal.
-        * @throws BadStateChangeException
-        *             If the run is not in the {@link Status#Initialized
-        *             Initialized} state
-        */
-       @WSDLDocumentation("Tells the given run to use the given 
already-uploaded Baclava file for all inputs.")
-       void setRunInputBaclavaFile(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "baclavaFileName") String fileName)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, BadStateChangeException;
-
-       /**
-        * Tells the run to use the given file for input on the given port. This
-        * overrides any previously set file or value on the port and causes the
-        * server to forget about using a Baclava file for all inputs.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param portName
-        *            The port to use the file for.
-        * @param portFilename
-        *            The file to use on the port. Must not start with a 
<tt>/</tt>
-        *            or contain a <tt>..</tt> element.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the run.
-        * @throws FilesystemAccessException
-        *             If the filename is illegal.
-        * @throws BadStateChangeException
-        *             If the run is not in the {@link Status#Initialized
-        *             Initialized} state.
-        * @throws BadPropertyValueException
-        *             If the input port may not be changed to the contents of 
the
-        *             given file.
-        */
-       @WSDLDocumentation("Tells the given run to use the given file for input 
on the given port.")
-       void setRunInputPortFile(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "portName") @XmlElement(required = 
true) String portName,
-                       @WebParam(name = "portFileName") @XmlElement(required = 
true) String portFilename)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, BadStateChangeException,
-                       BadPropertyValueException;
-
-       /**
-        * Tells the run to use the given value for input on the given port. 
This
-        * overrides any previously set file or value on the port and causes the
-        * server to forget about using a Baclava file for all inputs. Note that
-        * this is wholly unsuitable for use with binary data.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param portName
-        *            The port to use the file for.
-        * @param portValue
-        *            The literal value to use on the port.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the run.
-        * @throws BadStateChangeException
-        *             If the run is not in the {@link Status#Initialized
-        *             Initialized} state.
-        * @throws BadPropertyValueException
-        *             If the input port may not be changed to the given literal
-        *             value.
-        */
-       @WSDLDocumentation("Tells the given run to use the given literal string 
value for input on the given port.")
-       void setRunInputPortValue(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "portName") @XmlElement(required = 
true) String portName,
-                       @WebParam(name = "portValue") @XmlElement(required = 
true) String portValue)
-                       throws UnknownRunException, NoUpdateException,
-                       BadStateChangeException, BadPropertyValueException;
-
-       /**
-        * Tells the given run to use the given list delimiter (a 
single-character
-        * string value) for splitting the input on the given port. Note that
-        * nullability of the delimiter is supported here.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param portName
-        *            The port to set the list delimiter for.
-        * @param delimiter
-        *            The single-character value (in range U+00001..U+0007F) to 
use
-        *            as the delimiter, or <tt>null</tt> for no delimiter at 
all.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the run.
-        * @throws BadStateChangeException
-        *             If the run is not in the {@link Status#Initialized
-        *             Initialized} state.
-        * @throws BadPropertyValueException
-        *             If the delimiter may not be changed to the given literal
-        *             value.
-        */
-       @WSDLDocumentation("Tells the given run to use the given list delimiter 
(a single-character string value) for splitting the input on the given port. 
Note that nullability of the delimiter is supported here.")
-       void setRunInputPortListDelimiter(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "portName") @XmlElement(required = 
true) String portName,
-                       @WebParam(name = "delimiter") String delimiter)
-                       throws UnknownRunException, NoUpdateException,
-                       BadStateChangeException, BadPropertyValueException;
-
-       /**
-        * Get the Baclava file where the output of the run will be written.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The filename, or <tt>null</tt> if the results will be 
written to
-        *         a subdirectory <tt>out</tt> of the run's working directory.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "OutputBaclavaFile")
-       @WSDLDocumentation("Get the Baclava file where the output of the run 
will be written.")
-       String getRunOutputBaclavaFile(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Set the Baclava file where the output of the run will be written.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param outputFile
-        *            The filename for the Baclava file, or <tt>null</tt> or the
-        *            empty string to indicate that the results are to be 
written to
-        *            the subdirectory <tt>out</tt> of the run's working 
directory.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the run.
-        * @throws FilesystemAccessException
-        *             If the filename is illegal (starts with a <tt>/</tt> or
-        *             contains a <tt>..</tt> element.
-        * @throws BadStateChangeException
-        *             If the run is not in the {@link Status#Initialized
-        *             Initialized} state
-        */
-       @WSDLDocumentation("Set the Baclava file where the output of the run 
will be written.")
-       void setRunOutputBaclavaFile(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "baclavaFileName") String outputFile)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, BadStateChangeException;
-
-       /**
-        * Return a description of the outputs of a run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return Description document (higher level than filesystem traverse).
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws BadStateChangeException
-        *             If the run is in the {@link Status#Initialized 
Initialized}
-        *             state
-        * @throws FilesystemAccessException
-        *             If there is an exception when accessing the filesystem.
-        * @throws NoDirectoryEntryException
-        *             If things are odd in the filesystem.
-        */
-       @WebResult(name = "OutputDescription")
-       @WSDLDocumentation("Return a description of the outputs of a run. Only 
known during/after the run.")
-       OutputDescription getRunOutputDescription(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException, BadStateChangeException,
-                       FilesystemAccessException, NoDirectoryEntryException;
-
-       /**
-        * Get the time when the run will be eligible to be automatically 
deleted.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return A date at which the expiry will be scheduled. The actual 
deletion
-        *         will happen an arbitrary amount of time later (depending on
-        *         system policy).
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "Expiry")
-       @WSDLDocumentation("Get the time when the run will be eligible to be 
automatically deleted.")
-       Date getRunExpiry(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Set when the run will be eligible to be automatically deleted.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param expiry
-        *            A date at which the expiry will be scheduled. The actual
-        *            deletion will happen an arbitrary amount of time later
-        *            (depending on system policy).
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the lifetime of 
the
-        *             run.
-        */
-       @WSDLDocumentation("Set when the run will be eligible to be 
automatically deleted.")
-       void setRunExpiry(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "expiry") @XmlElement(required = true) 
Date expiry)
-                       throws UnknownRunException, NoUpdateException;
-
-       /**
-        * Get the time when the run was created.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The moment when the run was created (modulo some internal
-        *         overhead).
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "CreationTime")
-       @WSDLDocumentation("Get the time when the run was created.")
-       Date getRunCreationTime(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Get the time when the run was started.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The moment when the run was started (modulo some internal
-        *         overhead) or <tt>null</tt> to indicate that it has never 
started.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "StartTime")
-       @WSDLDocumentation("Get the time when the run was started.")
-       Date getRunStartTime(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Get the time when the run was detected as having finished.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The moment when the run was believed stopped. Note that this 
may
-        *         not be when the run <i>actually</i> finished; promptness of
-        *         detection depends on many factors.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "FinishTime")
-       @WSDLDocumentation("Get the time when the run was detected as having 
finished.")
-       Date getRunFinishTime(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Get the current status of the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The status code.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "Status")
-       @WSDLDocumentation("Get the current status of the given workflow run.")
-       Status getRunStatus(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Set the status of a run. This is used to start it executing, make it 
stop
-        * executing, etc. Note that changing the status of a run can 
<i>never</i>
-        * cause the run to be destroyed.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param status
-        *            The status to change to. Changing to the current status 
will
-        *            always have no effect.
-        * @return An empty string if the state change was completed, or a
-        *         description (never empty) of why the state change is ongoing.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the run.
-        * @throws BadStateChangeException
-        *             If the state change requested is impossible.
-        */
-       @WebResult(name = "PartialityReason")
-       @WSDLDocumentation("Set the status of a given workflow run.")
-       String setRunStatus(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "status") @XmlElement(required = true) 
Status status)
-                       throws UnknownRunException, NoUpdateException,
-                       BadStateChangeException;
-
-       /**
-        * Get the names of the event listeners attached to the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The listener names.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "ListenerName")
-       @WSDLDocumentation("Get the names of the event listeners attached to 
the run.")
-       String[] getRunListeners(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Adds an event listener to the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param listenerType
-        *            The type of event listener to add. Must be one of the 
names
-        *            returned by the {@link #getServerListeners()} operation.
-        * @param configuration
-        *            The configuration document for the event listener; the
-        *            interpretation of the configuration is up to the listener.
-        * @return The actual name of the listener.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user isn't allowed to manipulate the run.
-        * @throws NoListenerException
-        *             If the listener construction fails (<i>e.g.</i>, due to 
an
-        *             unsupported <b>listenerType</b> or a problem with the
-        *             <b>configuration</b>).
-        */
-       @WebResult(name = "ListenerName")
-       @WSDLDocumentation("Adds an event listener to the run.")
-       String addRunListener(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "listenerType") @XmlElement(required = 
true) String listenerType,
-                       @WebParam(name = "configuration") @XmlElement(required 
= true) String configuration)
-                       throws UnknownRunException, NoUpdateException, 
NoListenerException;
-
-       /**
-        * Returns the standard output of the workflow run. Unstarted runs 
return
-        * the empty string.
-        * <p>
-        * The equivalent thing can also be fetched from the relevant listener
-        * property (i.e., io/stdout).
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return Whatever the run engine printed on its stdout.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "StandardOutput")
-       @WSDLDocumentation("Returns the stdout from the run engine.")
-       String getRunStdout(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Returns the standard error of the workflow run. Unstarted runs 
return the
-        * empty string.
-        * <p>
-        * The equivalent thing can also be fetched from the relevant listener
-        * property (i.e., io/stderr).
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return Whatever the run engine printed on its stderr.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "StandardError")
-       @WSDLDocumentation("Returns the stderr from the run engine.")
-       String getRunStderr(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Returns the usage record for the workflow run. Unfinished runs return
-        * <tt>null</tt>.
-        * <p>
-        * The equivalent thing can also be fetched from the relevant listener
-        * property (i.e., io/usage).
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The usage record, or <tt>null</tt>.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "ResourceUsage")
-       @WSDLDocumentation("Returns the resource usage from the run engine.")
-       JobUsageRecord getRunUsageRecord(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Returns the log of the workflow run. Unstarted runs return the empty
-        * string.
-        * <p>
-        * This can also be fetched from the appropriate file (i.e.,
-        * <tt>logs/detail.log</tt>).
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return Whatever the run engine wrote to its log.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "Log")
-       @WSDLDocumentation("Returns the detailed log from the run engine.")
-       String getRunLog(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Returns the run bundle of a run. The run must be <i>finished</i> for 
this
-        * to be guaranteed to be present, and must <i>not</i> have had its 
output
-        * generated as Baclava.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The contents of the run bundle.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If there was a problem reading the bundle.
-        * @throws NoDirectoryEntryException
-        *             If the bundle doesn't exist currently.
-        */
-       @WebResult(name = "RunBundle")
-       @WSDLDocumentation("Gets the run bundle of a finished run. MTOM support 
recommended!")
-       FileContents getRunBundle(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Gets whether to generate provenance (in a run bundle) for a run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return Whether provenance will be generated.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "GenerateProvenance")
-       @WSDLDocumentation("Gets whether a run generates provenance.")
-       boolean getRunGenerateProvenance(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Sets whether to generate provenance (in a run bundle) for a run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param generateProvenance
-        *            Whether to generate provenance.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user is not allowed to manipulate the run.
-        */
-       @WSDLDocumentation("Sets whether a run generates provenance. "
-                       + "Only usefully settable before the run is started.")
-       void setRunGenerateProvenance(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "generateProvenance") 
@XmlElement(required = true) boolean generateProvenance)
-                       throws UnknownRunException, NoUpdateException;
-
-       /**
-        * Get the owner of the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The status code.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        */
-       @WebResult(name = "Owner")
-       @WSDLDocumentation("Get the owner of the given workflow run.")
-       String getRunOwner(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException;
-
-       /**
-        * Get the list of permissions associated with a workflow run.
-        * 
-        * @param runName
-        *            The name of the run whose permissions are to be obtained.
-        * @return A description of the non-<tt>none</tt> permissions.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the 
current
-        *             user is not permitted to see it.
-        * @throws NotOwnerException
-        *             If asked to provide this information about a run that the
-        *             current user may see but where they are not the owner of 
it.
-        */
-       @WebResult(name = "PermissionList")
-       @WSDLDocumentation("Get the list of permissions associated with a given 
workflow run.")
-       PermissionList listRunPermissions(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException, NotOwnerException;
-
-       /**
-        * Set the permission for a user to access and update a particular 
workflow
-        * run.
-        * 
-        * @param runName
-        *            The name of the run whose permissions are to be updated.
-        * @param userName
-        *            The name of the user about whom this call is talking.
-        * @param permission
-        *            The permission level to set.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the 
current
-        *             user is not permitted to see it.
-        * @throws NotOwnerException
-        *             If asked to provide this information about a run that the
-        *             current user may see but where they are not the owner of 
it.
-        */
-       @WSDLDocumentation("Set the permission for a user to access and update 
a given workflow run.")
-       void setRunPermission(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "userName") @XmlElement(required = 
true) String userName,
-                       @WebParam(name = "permission") @XmlElement(required = 
true) Permission permission)
-                       throws UnknownRunException, NotOwnerException;
-
-       /**
-        * Get the credentials associated with the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The collection of credentials.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NotOwnerException
-        *             If the user is permitted to see the run, but isn't the 
owner;
-        *             only the owner may see the credentials.
-        */
-       @WebResult(name = "Credentials")
-       @WSDLDocumentation("Get the credentials (passwords, private keys) 
associated with the given workflow run. Only the owner may do this.")
-       Credential[] getRunCredentials(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException, NotOwnerException;
-
-       /**
-        * Set a credential associated with the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param credentialID
-        *            The handle of the credential to set. If empty, a new
-        *            credential will be created.
-        * @param credential
-        *            The credential to set.
-        * @return The handle of the credential that was created or updated.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NotOwnerException
-        *             If the user is permitted to see the run, but isn't the 
owner;
-        *             only the owner may manipulate the credentials.
-        * @throws InvalidCredentialException
-        *             If the <b>credential</b> fails its checks.
-        * @throws NoCredentialException
-        *             If the <b>credentialID</b> is not empty but does not
-        *             correspond to an existing credential.
-        * @throws BadStateChangeException
-        *             If an attempt to manipulate the credentials is done 
after the
-        *             workflow has started running.
-        */
-       @WebResult(name = "credentialID")
-       @WSDLDocumentation("Set a credential (password, private key, etc.) 
associated with the given run. Only the owner may do this.")
-       String setRunCredential(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "credentialID") @XmlElement(required = 
true) String credentialID,
-                       @WebParam(name = "credential") @XmlElement(required = 
true) Credential credential)
-                       throws UnknownRunException, NotOwnerException,
-                       InvalidCredentialException, NoCredentialException,
-                       BadStateChangeException;
-
-       /**
-        * Delete a credential associated with the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param credentialID
-        *            The handle of the credential to delete. If empty, a new
-        *            credential will be created.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NotOwnerException
-        *             If the user is permitted to see the run, but isn't the 
owner;
-        *             only the owner may manipulate the credentials.
-        * @throws NoCredentialException
-        *             If the given credentialID does not exist.
-        * @throws BadStateChangeException
-        *             If an attempt to manipulate the credentials is done 
after the
-        *             workflow has started running.
-        */
-       @WSDLDocumentation("Delete a credential associated with the given run. 
Only the owner may do this.")
-       void deleteRunCredential(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "credentialID") @XmlElement(required = 
true) String credentialID)
-                       throws UnknownRunException, NotOwnerException,
-                       NoCredentialException, BadStateChangeException;
-
-       /**
-        * Get the certificate collections associated with the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @return The collection of credentials.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NotOwnerException
-        *             If the user is permitted to see the run, but isn't the 
owner;
-        *             only the owner may see the credentials.
-        */
-       @WebResult(name = "CertificateCollections")
-       @WSDLDocumentation("Get the trusted (server or CA) certificates 
associated with the run. Only the owner may do this.")
-       Trust[] getRunCertificates(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName)
-                       throws UnknownRunException, NotOwnerException;
-
-       /**
-        * Set a certificate collection associated with the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param certificateID
-        *            The handle of the certificate collection to set. If 
empty, a
-        *            new certificate collection will be created.
-        * @param certificate
-        *            The certificate collection to set.
-        * @return The handle of the certificate set that was created or 
updated.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NotOwnerException
-        *             If the user is permitted to see the run, but isn't the 
owner;
-        *             only the owner may manipulate the certificates.
-        * @throws InvalidCredentialException
-        *             If the <b>certificate</b> fails its checks.
-        * @throws NoCredentialException
-        *             If the <b>credentialID</b> is not empty but does not
-        *             correspond to an existing certificate collection.
-        * @throws BadStateChangeException
-        *             If an attempt to manipulate the credentials is done 
after the
-        *             workflow has started running.
-        */
-       @WebResult(name = "certificateID")
-       @WSDLDocumentation("Set a trusted (server or CA) certificate associated 
with the run. Only the owner may do this.")
-       String setRunCertificates(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "certificateID") String certificateID,
-                       @WebParam(name = "certificate") @XmlElement(required = 
true) Trust certificate)
-                       throws UnknownRunException, NotOwnerException,
-                       InvalidCredentialException, NoCredentialException,
-                       BadStateChangeException;
-
-       /**
-        * Delete a certificate collection associated with the run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param certificateID
-        *            The handle of the credential to delete.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NotOwnerException
-        *             If the user is permitted to see the run, but isn't the 
owner;
-        *             only the owner may manipulate the certificates.
-        * @throws NoCredentialException
-        *             If the given certificateID does not exist.
-        * @throws BadStateChangeException
-        *             If an attempt to manipulate the credentials is done 
after the
-        *             workflow has started running.
-        */
-       @WSDLDocumentation("Delete a trusted (server or CA) certificate 
associated with the run. Only the owner may do this.")
-       void deleteRunCertificates(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "certificateID") @XmlElement(required 
= true) String certificateID)
-                       throws UnknownRunException, NotOwnerException,
-                       NoCredentialException, BadStateChangeException;
-
-       /**
-        * Get the contents of any directory at/under the run's working 
directory.
-        * Runs do not share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param directory
-        *            The name of the directory to fetch; the main working 
directory
-        *            is <tt>/</tt> and <tt>..</tt> is always disallowed.
-        * @return A list of entries. They are assumed to be all directories or
-        *         files.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., reading the 
contents of
-        *             a file).
-        * @throws NoDirectoryEntryException
-        *             If the name of the directory can't be looked up.
-        */
-       @WebResult(name = "DirectoryEntry")
-       @WSDLDocumentation("Get the contents of any directory at/under the 
run's working directory.")
-       DirEntry[] getRunDirectoryContents(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "directory") @XmlElement(required = 
true) DirEntry directory)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Get the contents of any directory (and its subdirectories) at/under 
the
-        * run's working directory, returning it as a compressed ZIP file. Runs 
do
-        * not share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param directory
-        *            The name of the directory to fetch; the main working 
directory
-        *            is <tt>/</tt> and <tt>..</tt> is always disallowed.
-        * @return A serialized ZIP file.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., reading the 
contents of
-        *             a file).
-        * @throws NoDirectoryEntryException
-        *             If the name of the directory can't be looked up.
-        */
-       @WebResult(name = "ZipFile")
-       @WSDLDocumentation("Get the contents of any directory (and its 
subdirectories) at/under the run's working directory, returning it as a 
compressed ZIP file.")
-       byte[] getRunDirectoryAsZip(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "directory") @XmlElement(required = 
true) DirEntry directory)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Get the contents of any directory (and its subdirectories) at/under 
the
-        * run's working directory, returning it as a compressed ZIP file that 
is
-        * streamed via MTOM. Runs do not share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param directory
-        *            The name of the directory to fetch; the main working 
directory
-        *            is <tt>/</tt> and <tt>..</tt> is always disallowed.
-        * @return An MTOM-streamable ZIP file reference.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., reading the 
contents of
-        *             a file).
-        * @throws NoDirectoryEntryException
-        *             If the name of the directory can't be looked up.
-        */
-       @WebResult(name = "ZipStream")
-       @WSDLDocumentation("Get the contents of any directory (and its 
subdirectories) at/under the run's working directory, returning it as a 
compressed ZIP file that is streamed by MTOM.")
-       ZippedDirectory getRunDirectoryAsZipMTOM(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "directory") @XmlElement(required = 
true) DirEntry directory)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Make a new empty directory beneath an existing one, which must be the
-        * run's working directory or a directory beneath it. Runs do not share
-        * working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param parent
-        *            The parent directory that will have the new directory 
added
-        *            beneath it.
-        * @param name
-        *            The name of the directory to create. Must not be the same 
as
-        *            any other file or directory in the <i>parent</i> 
directory.
-        *            The name <i>must not</i> consist of <tt>..</tt> or have a
-        *            <tt>/</tt> in it.
-        * @return A reference to the created directory.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user is not allowed to make modifications to the 
run.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., making something 
with
-        *             the same name as something that already exists).
-        * @throws NoDirectoryEntryException
-        *             If the name of the containing directory can't be looked 
up.
-        */
-       @WebResult(name = "CreatedDirectory")
-       @WSDLDocumentation("Make a new empty directory beneath an existing one, 
all relative to the given run's main working directory.")
-       DirEntry makeRunDirectory(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "parentDirectory") 
@XmlElement(required = true) DirEntry parent,
-                       @WebParam(name = "directoryName") @XmlElement(required 
= true) String name)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, NoDirectoryEntryException;
-
-       /**
-        * Make a new empty file in an existing directory, which may be the 
run's
-        * working directory or any directory beneath it. Runs do not share 
working
-        * directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param parent
-        *            The parent directory that will have the new file added to 
it.
-        * @param name
-        *            The name of the file to create. Must not be the same as 
any
-        *            other file or directory in the <i>parent</i> directory. 
The
-        *            name <i>must not</i> consist of <tt>..</tt> or have a
-        *            <tt>/</tt> in it.
-        * @return A reference to the created file. The file will be empty.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user is not allowed to make modifications to the 
run.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., making something 
with
-        *             the same name as something that already exists).
-        * @throws NoDirectoryEntryException
-        *             If the name of the containing directory can't be looked 
up.
-        */
-       @WebResult(name = "CreatedFile")
-       @WSDLDocumentation("Make a new empty file in an existing directory, 
which may be the run's working directory or any directory beneath it.")
-       DirEntry makeRunFile(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "parentDirectory") 
@XmlElement(required = true) DirEntry parent,
-                       @WebParam(name = "fileNameTail") @XmlElement(required = 
true) String name)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, NoDirectoryEntryException;
-
-       /**
-        * Destroy an entry (file or directory) in or beneath a run's working
-        * directory. Runs do not share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param dirEntry
-        *            Reference to an existing item in a directory that will be
-        *            destroyed. May be a reference to either a file or a 
directory.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user is not allowed to make modifications to the 
run.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., deleting something
-        *             which doesn't exist or attempting to delete the main 
working
-        *             directory).
-        * @throws NoDirectoryEntryException
-        *             If the name of the file or directory can't be looked up.
-        */
-       @WSDLDocumentation("Destroy an entry (file or directory) in or beneath 
a run's working directory.")
-       void destroyRunDirectoryEntry(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "directoryEntry") @XmlElement(required 
= true) DirEntry dirEntry)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, NoDirectoryEntryException;
-
-       /**
-        * Get the contents of a file under the run's working directory. Runs 
do not
-        * share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param file
-        *            The name of the file to fetch; the main working directory 
is
-        *            <tt>/</tt> and <tt>..</tt> is always disallowed.
-        * @return The literal byte contents of the file.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., reading the 
contents of
-        *             a directory).
-        * @throws NoDirectoryEntryException
-        *             If the file doesn't exist.
-        */
-       @WebResult(name = "FileContents")
-       @WSDLDocumentation("Get the contents of a file under the run's working 
directory.")
-       byte[] getRunFileContents(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "fileName") @XmlElement(required = 
true) DirEntry file)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Get the contents of a file under the run's working directory via 
MTOM.
-        * Runs do not share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param file
-        *            The name of the file to fetch; the main working directory 
is
-        *            <tt>/</tt> and <tt>..</tt> is always disallowed.
-        * @return The contents, described for transfer via MTOM.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., reading the 
contents of
-        *             a directory).
-        * @throws NoDirectoryEntryException
-        *             If the file doesn't exist.
-        */
-       @WebResult(name = "FileContentsMTOM")
-       @WSDLDocumentation("Get the contents of a file via MTOM.")
-       FileContents getRunFileContentsMTOM(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "fileName") @XmlElement(required = 
true) DirEntry file)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Set the contents of a file under the run's working directory. Runs 
do not
-        * share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param file
-        *            The name of the file to update; the main working 
directory is
-        *            <tt>/</tt> and <tt>..</tt> is always disallowed.
-        * @param newContents
-        *            The literal bytes to set the file contents to.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user is not allowed to make modifications to the 
run.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., writing the 
contents of
-        *             a directory).
-        * @throws NoDirectoryEntryException
-        *             If the file doesn't exist.
-        */
-       @WSDLDocumentation("Set the contents of a file under the run's working 
directory.")
-       void setRunFileContents(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "fileName") @XmlElement(required = 
true) DirEntry file,
-                       @WebParam(name = "contents") @XmlElement(required = 
true) byte[] newContents)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, NoDirectoryEntryException;
-
-       /**
-        * Set the contents of a file under the run's working directory. Runs 
do not
-        * share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param newContents
-        *            The description of what file to set, and what to the file
-        *            contents should be set to.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user is not allowed to make modifications to the 
run.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., writing the 
contents of
-        *             a directory).
-        * @throws NoDirectoryEntryException
-        *             If the file doesn't exist.
-        */
-       @WSDLDocumentation("Set the contents of a file under the run's working 
directory.")
-       void setRunFileContentsMTOM(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "contents") @XmlElement(required = 
true) FileContents newContents)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, NoDirectoryEntryException;
-
-       /**
-        * Set the contents of a file under the run's working directory to the
-        * contents of a publicly readable URI. Runs do not share working
-        * directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param file
-        *            The name of the file to update; the main working 
directory is
-        *            <tt>/</tt> and <tt>..</tt> is always disallowed.
-        * @param reference
-        *            The publicly readable URI whose contents are to become the
-        *            literal bytes of the file's contents.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoUpdateException
-        *             If the user is not allowed to make modifications to the 
run.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., writing the 
contents of
-        *             a directory).
-        * @throws NoDirectoryEntryException
-        *             If the file doesn't exist.
-        */
-       @WSDLDocumentation("Set the contents of a file under the run's working 
directory from the contents of a publicly readable URI.")
-       void setRunFileContentsFromURI(@WebParam(name = "runName") String 
runName,
-                       @WebParam(name = "fileName") DirEntryReference file,
-                       @WebParam(name = "contents") URI reference)
-                       throws UnknownRunException, NoUpdateException,
-                       FilesystemAccessException, NoDirectoryEntryException;
-
-       /**
-        * Get the length of any file (in bytes) at/under the run's working
-        * directory. Runs do not share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param file
-        *            The name of the file to get the length of; the main 
working
-        *            directory is <tt>/</tt> and <tt>..</tt> is always 
disallowed.
-        * @return The number of bytes in the file.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., reading the length 
of a
-        *             directory).
-        * @throws NoDirectoryEntryException
-        *             If the file doesn't exist.
-        */
-       @WebResult(name = "FileLength")
-       @WSDLDocumentation("Get the length of any file (in bytes) at/under the 
run's working directory.")
-       long getRunFileLength(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "fileName") @XmlElement(required = 
true) DirEntry file)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Get the time that the file or directory (at/under the run's working
-        * directory) was last modified. Runs do not share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param file
-        *            The name of the file to get the modification date of; the 
main
-        *            working directory is <tt>/</tt> and <tt>..</tt> is always
-        *            disallowed.
-        * @return The modification date of the file or directory, as 
understood by
-        *         the underlying operating system.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated.
-        * @throws NoDirectoryEntryException
-        *             If the file or directory doesn't exist.
-        */
-       @WebResult(name = "FileModified")
-       @WSDLDocumentation("Get the length of any file (in bytes) at/under the 
run's working directory.")
-       Date getRunFileModified(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "fileName") @XmlElement(required = 
true) DirEntry file)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Get the content type of any file at/under the run's working 
directory.
-        * Runs do not share working directories.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param file
-        *            The name of the file to get the length of; the main 
working
-        *            directory is <tt>/</tt> and <tt>..</tt> is always 
disallowed.
-        * @return The content type of the file.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws FilesystemAccessException
-        *             If some assumption is violated (e.g., reading the length 
of a
-        *             directory).
-        * @throws NoDirectoryEntryException
-        *             If the file doesn't exist.
-        */
-       @WebResult(name = "FileContentType")
-       @WSDLDocumentation("Get the content type of any file at/under the run's 
working directory.")
-       String getRunFileType(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "fileName") @XmlElement(required = 
true) DirEntry file)
-                       throws UnknownRunException, FilesystemAccessException,
-                       NoDirectoryEntryException;
-
-       /**
-        * Get the configuration document for an event listener attached to a 
run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param listenerName
-        *            The name of the listener attached.
-        * @return The configuration document.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoListenerException
-        *             If no such listener exists.
-        */
-       @WebResult(name = "ListenerConfiguration")
-       @WSDLDocumentation("Get the configuration document for an event 
listener attached to a run.")
-       String getRunListenerConfiguration(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "listenerName") @XmlElement(required = 
true) String listenerName)
-                       throws UnknownRunException, NoListenerException;
-
-       /**
-        * Get the list of properties supported by an event listener attached 
to a
-        * run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param listenerName
-        *            The name of the listener attached.
-        * @return The list of property names.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoListenerException
-        *             If no such listener exists.
-        */
-       @WebResult(name = "ListenerPropertyName")
-       @WSDLDocumentation("Get the list of properties supported by an event 
listener attached to a run.")
-       String[] getRunListenerProperties(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "listenerName") @XmlElement(required = 
true) String listenerName)
-                       throws UnknownRunException, NoListenerException;
-
-       /**
-        * Get the value of a property for an event listener attached to a run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param listenerName
-        *            The name of the listener attached.
-        * @param propertyName
-        *            The name of the property to read.
-        * @return The configuration document.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoListenerException
-        *             If no such listener exists or if the listener has no such
-        *             property.
-        */
-       @WebResult(name = "ListenerPropertyValue")
-       @WSDLDocumentation("Get the value of a property for an event listener 
attached to a run.")
-       String getRunListenerProperty(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "listenerName") @XmlElement(required = 
true) String listenerName,
-                       @WebParam(name = "propertyName") @XmlElement(required = 
true) String propertyName)
-                       throws UnknownRunException, NoListenerException;
-
-       /**
-        * Set the value of a property for an event listener attached to a run.
-        * 
-        * @param runName
-        *            The handle of the run.
-        * @param listenerName
-        *            The name of the listener attached.
-        * @param propertyName
-        *            The name of the property to write.
-        * @param value
-        *            The value to set the property to.
-        * @throws UnknownRunException
-        *             If the server doesn't know about the run or if the user 
is
-        *             not permitted to see it.
-        * @throws NoListenerException
-        *             If no such listener exists, the listener has no such
-        *             property, or the value is considered "unacceptable" in 
some
-        *             way.
-        * @throws NoUpdateException
-        *             If the user is not allowed to make modifications to the 
run.
-        */
-       @WSDLDocumentation("Set the value of a property for an event listener 
attached to a run.")
-       void setRunListenerProperty(
-                       @WebParam(name = "runName") @XmlElement(required = 
true) String runName,
-                       @WebParam(name = "listenerName") @XmlElement(required = 
true) String listenerName,
-                       @WebParam(name = "propertyName") @XmlElement(required = 
true) String propertyName,
-                       @WebParam(name = "propertyValue") @XmlElement(required 
= true) String value)
-                       throws UnknownRunException, NoUpdateException, 
NoListenerException;
-
-       /**
-        * Gets the status of the server. Follows the HELIO Monitoring Service
-        * protocol.
-        * 
-        * @return A status string.
-        */
-       @WSDLDocumentation("A simple way to get the status of the overall 
server.")
-       @WebResult(name = "ServerStatus")
-       String getServerStatus();
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-webapp/src/main/java/org/taverna/server/master/soap/WrappedWorkflow.java
----------------------------------------------------------------------
diff --git 
a/server-webapp/src/main/java/org/taverna/server/master/soap/WrappedWorkflow.java
 
b/server-webapp/src/main/java/org/taverna/server/master/soap/WrappedWorkflow.java
deleted file mode 100644
index cd06115..0000000
--- 
a/server-webapp/src/main/java/org/taverna/server/master/soap/WrappedWorkflow.java
+++ /dev/null
@@ -1,156 +0,0 @@
-/*
- * Copyright (C) 2012 The University of Manchester
- * 
- * See the file "LICENSE.txt" for license terms.
- */
-package org.taverna.server.master.soap;
-
-import static javax.xml.bind.annotation.XmlAccessType.NONE;
-import static org.apache.commons.io.IOUtils.closeQuietly;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.PipedInputStream;
-import java.io.PipedOutputStream;
-
-import javax.activation.DataHandler;
-import javax.activation.DataSource;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlMimeType;
-import javax.xml.bind.annotation.XmlTransient;
-import javax.xml.bind.annotation.XmlType;
-
-import org.taverna.server.master.common.Workflow;
-
-import uk.org.taverna.scufl2.api.io.ReaderException;
-import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
-import uk.org.taverna.scufl2.api.io.WriterException;
-
-/**
- * An MTOM-capable description of how to transfer the contents of a file.
- * 
- * @author Donal Fellows
- */
-@XmlType(name = "WorkflowReference")
-@XmlAccessorType(NONE)
-public class WrappedWorkflow {
-       @XmlMimeType("application/octet-stream")
-       // JAXB bug: must be this
-       public DataHandler workflowData;
-       Workflow workflow;
-
-       /**
-        * Initialize the contents of this descriptor from the given file and
-        * content type.
-        * 
-        * @param workflow
-        *            The workflow that is to be reported.
-        */
-       public void setWorkflow(Workflow workflow) {
-               workflowData = new DataHandler(new WorkflowSource(workflow));
-       }
-
-       @XmlTransient
-       public Workflow getWorkflow() throws IOException {
-               if (workflow != null)
-                       return workflow;
-               try {
-                       return new Workflow(new WorkflowBundleIO().readBundle(
-                                       workflowData.getInputStream(), null));
-               } catch (ReaderException e) {
-                       throw new IOException("problem converting to scufl2 
bundle", e);
-               }
-       }
-}
-
-/**
- * A data source that knows how to deliver a workflow.
- * 
- * @author Donal Fellows
- */
-class WorkflowSource implements DataSource {
-       WorkflowSource(Workflow workflow) {
-               this.wf = workflow;
-               this.io = new WorkflowBundleIO();
-       }
-
-       Workflow wf;
-       final WorkflowBundleIO io;
-
-       @Override
-       public String getContentType() {
-               return wf.getPreferredContentType().getContentType();
-       }
-
-       @Override
-       public String getName() {
-               switch (wf.getPreferredContentType()) {
-               case SCUFL2:
-                       return "workflow.scufl2";
-               case T2FLOW:
-                       return "workflow.t2flow";
-               default:
-                       return "workflow";
-               }
-       }
-
-       @Override
-       public InputStream getInputStream() throws IOException {
-               PipedInputStream is = new PipedInputStream();
-               final OutputStream os = new PipedOutputStream(is);
-               new Worker() {
-                       @Override
-                       public void doWork() throws WriterException, 
IOException {
-                               io.writeBundle(wf.getScufl2Workflow(), os, wf
-                                               
.getPreferredContentType().getContentType());
-                       }
-
-                       @Override
-                       public void doneWork() {
-                               closeQuietly(os);
-                       }
-               };
-               return is;
-       }
-
-       @Override
-       public OutputStream getOutputStream() throws IOException {
-               final PipedInputStream is = new PipedInputStream();
-               OutputStream os = new PipedOutputStream(is);
-               new Worker() {
-                       @Override
-                       public void doWork() throws IOException, 
ReaderException {
-                               wf = new Workflow(io.readBundle(is, null));
-                       }
-
-                       @Override
-                       public void doneWork() {
-                               closeQuietly(is);
-                       }
-               };
-               return os;
-       }
-
-       static abstract class Worker extends Thread {
-               public Worker() {
-                       setDaemon(true);
-                       start();
-               }
-
-               public abstract void doWork() throws Exception;
-
-               public abstract void doneWork();
-
-               @Override
-               public void run() {
-                       try {
-                               doWork();
-                       } catch (Exception e) {
-                               // do nothing.
-                       } finally {
-                               doneWork();
-                       }
-               }
-       }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-webapp/src/main/java/org/taverna/server/master/soap/ZippedDirectory.java
----------------------------------------------------------------------
diff --git 
a/server-webapp/src/main/java/org/taverna/server/master/soap/ZippedDirectory.java
 
b/server-webapp/src/main/java/org/taverna/server/master/soap/ZippedDirectory.java
deleted file mode 100644
index 90fe51b..0000000
--- 
a/server-webapp/src/main/java/org/taverna/server/master/soap/ZippedDirectory.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
- * Copyright (C) 2012 The University of Manchester
- * 
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.soap;
-
-import static org.taverna.server.master.api.ContentTypes.APPLICATION_ZIP_TYPE;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-
-import javax.activation.DataHandler;
-import javax.activation.DataSource;
-import javax.activation.UnsupportedDataTypeException;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlMimeType;
-import javax.xml.bind.annotation.XmlType;
-
-import org.taverna.server.master.exceptions.FilesystemAccessException;
-import org.taverna.server.master.interfaces.Directory;
-
-/**
- * An MTOM-capable description of how to transfer the zipped contents of a
- * directory.
- * 
- * @author Donal Fellows
- * @see Directory#getContentsAsZip()
- */
-@XmlType(name = "ZippedDirectory")
-public class ZippedDirectory {
-       @XmlElement
-       public String name;
-       @XmlMimeType("application/octet-stream")
-       // JAXB bug: must be this
-       public DataHandler fileData;
-
-       public ZippedDirectory() {
-       }
-
-       /**
-        * Initialise the contents of this descriptor from the given directory.
-        * 
-        * @param dir
-        *            The directory that is to be reported.
-        */
-       public ZippedDirectory(Directory dir) {
-               name = dir.getFullName();
-               fileData = new DataHandler(new ZipSource(dir));
-       }
-}
-
-/**
- * A data source that knows how to communicate with the Taverna Server 
back-end.
- * 
- * @author Donal Fellows
- */
-class ZipSource implements DataSource {
-       ZipSource(Directory d) {
-               this.d = d;
-       }
-
-       private final Directory d;
-
-       @Override
-       public String getContentType() {
-               return APPLICATION_ZIP_TYPE.toString();
-       }
-
-       @Override
-       public String getName() {
-               return d.getName();
-       }
-
-       @Override
-       public InputStream getInputStream() throws IOException {
-               try {
-                       return d.getContentsAsZip();
-               } catch (FilesystemAccessException e) {
-                       throw new IOException(e);
-               }
-       }
-
-       @Override
-       public OutputStream getOutputStream() throws IOException {
-               throw new UnsupportedDataTypeException();
-       }
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-webapp/src/main/java/org/taverna/server/master/soap/package-info.java
----------------------------------------------------------------------
diff --git 
a/server-webapp/src/main/java/org/taverna/server/master/soap/package-info.java 
b/server-webapp/src/main/java/org/taverna/server/master/soap/package-info.java
deleted file mode 100644
index 51d9b69..0000000
--- 
a/server-webapp/src/main/java/org/taverna/server/master/soap/package-info.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- * 
- * See the file "LICENSE" for license terms.
- */
-/**
- * This package contains the SOAP interface to Taverna Server.
- * @author Donal Fellows
- */
-@XmlSchema(namespace = SERVER_SOAP, elementFormDefault = QUALIFIED, 
attributeFormDefault = QUALIFIED, xmlns = {
-               @XmlNs(prefix = "xlink", namespaceURI = XLINK),
-               @XmlNs(prefix = "ts", namespaceURI = SERVER),
-               @XmlNs(prefix = "ts-rest", namespaceURI = SERVER_REST),
-               @XmlNs(prefix = "ts-soap", namespaceURI = SERVER_SOAP),
-               @XmlNs(prefix = "port", namespaceURI = DATA),
-               @XmlNs(prefix = "feed", namespaceURI = FEED),
-               @XmlNs(prefix = "admin", namespaceURI = ADMIN) })
-package org.taverna.server.master.soap;
-
-import static javax.xml.bind.annotation.XmlNsForm.QUALIFIED;
-import static org.taverna.server.master.common.Namespaces.ADMIN;
-import static org.taverna.server.master.common.Namespaces.FEED;
-import static org.taverna.server.master.common.Namespaces.SERVER;
-import static org.taverna.server.master.common.Namespaces.SERVER_REST;
-import static org.taverna.server.master.common.Namespaces.SERVER_SOAP;
-import static org.taverna.server.master.common.Namespaces.XLINK;
-import static org.taverna.server.port_description.Namespaces.DATA;
-
-import javax.xml.bind.annotation.XmlNs;
-import javax.xml.bind.annotation.XmlSchema;
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecord.java
----------------------------------------------------------------------
diff --git 
a/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecord.java 
b/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecord.java
deleted file mode 100644
index 487dbd0..0000000
--- 
a/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecord.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- * 
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.usage;
-
-import java.util.Date;
-
-import javax.jdo.annotations.Column;
-import javax.jdo.annotations.Index;
-import javax.jdo.annotations.PersistenceCapable;
-import javax.jdo.annotations.Persistent;
-import javax.jdo.annotations.PrimaryKey;
-import javax.jdo.annotations.Queries;
-import javax.jdo.annotations.Query;
-import javax.xml.bind.JAXBException;
-
-import org.ogf.usage.JobUsageRecord;
-
-/**
- * A usage record as recorded in the database.
- * 
- * @author Donal Fellows
- */
-@PersistenceCapable(table = "USAGE_RECORD_LOG", schema = "UR", cacheable = 
"true")
-@Queries({ @Query(name = "allByDate", value = "SELECT USAGE_RECORD FROM 
UR.USAGE_RECORD_LOG ORDER BY CREATE_DATE", resultClass = String.class, 
unmodifiable = "true", unique = "false", language = "SQL") })
-public class UsageRecord {
-       /**
-        * Create an empty usage record database entry.
-        */
-       public UsageRecord() {
-       }
-
-       /**
-        * Create a usage record database entry that is populated from the 
given UR.
-        * 
-        * @param usageRecord
-        *            The originating usage record.
-        * @throws JAXBException
-        *             If deserialization of the record fails.
-        */
-       public UsageRecord(String usageRecord) throws JAXBException {
-               JobUsageRecord jur = JobUsageRecord.unmarshal(usageRecord);
-               setUsageRecord(usageRecord);
-               setCreateDate(jur.getRecordIdentity().getCreateTime()
-                               .toGregorianCalendar().getTime());
-               setId(jur.getRecordIdentity().getRecordId());
-               setUserid(jur.getUserIdentity().get(0).getLocalUserId());
-       }
-
-       /**
-        * Create a usage record database entry that is populated from the 
given UR.
-        * 
-        * @param usageRecord
-        *            The originating usage record.
-        * @throws JAXBException
-        *             If serialization of the record fails.
-        */
-       public UsageRecord(JobUsageRecord usageRecord) throws JAXBException {
-               setUsageRecord(usageRecord.marshal());
-               setCreateDate(usageRecord.getRecordIdentity().getCreateTime()
-                               .toGregorianCalendar().getTime());
-               setId(usageRecord.getRecordIdentity().getRecordId());
-               
setUserid(usageRecord.getUserIdentity().get(0).getLocalUserId());
-       }
-
-       @PrimaryKey
-       @Column(name = "ID", length = 40)
-       private String id;
-
-       @Persistent
-       @Index(name = "USERID_IDX")
-       @Column(name = "USERID", length = 24)
-       private String userid;
-
-       @Persistent
-       @Index(name = "CREATE_IDX")
-       @Column(name = "CREATE_DATE")
-       private Date createDate;
-
-       @Persistent
-       @Column(name = "USAGE_RECORD", length = 32000)
-       // TODO Consider moving to BLOB (CLOB?) type
-       private String usageRecord;
-
-       public String getId() {
-               return id;
-       }
-
-       public void setId(String id) {
-               this.id = id;
-       }
-
-       public String getUserid() {
-               return userid;
-       }
-
-       public void setUserid(String userid) {
-               this.userid = userid;
-       }
-
-       public Date getCreateDate() {
-               return createDate;
-       }
-
-       public void setCreateDate(Date createDate) {
-               this.createDate = createDate;
-       }
-
-       public String getUsageRecord() {
-               return usageRecord;
-       }
-
-       public void setUsageRecord(String usageRecord) {
-               this.usageRecord = usageRecord;
-       }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java
----------------------------------------------------------------------
diff --git 
a/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java
 
b/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java
deleted file mode 100644
index 12de304..0000000
--- 
a/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- * 
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.usage;
-
-import static org.apache.commons.logging.LogFactory.getLog;
-
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.annotation.PreDestroy;
-import javax.xml.bind.JAXBException;
-
-import org.apache.commons.logging.Log;
-import org.ogf.usage.JobUsageRecord;
-import org.springframework.beans.factory.annotation.Required;
-import org.taverna.server.master.api.ManagementModel;
-import org.taverna.server.master.utils.Contextualizer;
-import org.taverna.server.master.utils.JDOSupport;
-
-/**
- * A simple state-aware writer of usage records. It just appends them, one by
- * one, to the file whose name is stored in the state.
- * 
- * @author Donal Fellows
- */
-public class UsageRecordRecorder extends JDOSupport<UsageRecord> {
-       private Log log = getLog("Taverna.Server.Webapp");
-       public UsageRecordRecorder() {
-               super(UsageRecord.class);
-       }
-
-       private String logFile = null;
-       private boolean disableDB = false;
-       private ManagementModel state;
-       private Contextualizer contextualizer;
-       private String logDestination;
-       private PrintWriter writer;
-       private Object lock = new Object();
-       private UsageRecordRecorder self;
-
-       /**
-        * @param state
-        *            the state to set
-        */
-       @Required
-       public void setState(ManagementModel state) {
-               this.state = state;
-       }
-
-       @Required
-       public void setSelf(UsageRecordRecorder self) {
-               this.self = self;
-       }
-
-       public void setLogFile(String logFile) {
-               this.logFile = (logFile == null || logFile.equals("none")) ? 
null : logFile;
-       }
-
-       public void setDisableDB(String disable) {
-               disableDB = "yes".equalsIgnoreCase(disable);
-       }
-
-       /**
-        * @param contextualizer
-        *            the system's contextualizer, used to allow making the UR 
dump
-        *            file be placed relative to the webapp.
-        */
-       @Required
-       public void setContextualizer(Contextualizer contextualizer) {
-               this.contextualizer = contextualizer;
-       }
-
-       /**
-        * Accept a usage record for recording.
-        * 
-        * @param usageRecord
-        *            The serialized usage record to record.
-        */
-       public void storeUsageRecord(String usageRecord) {
-               String logfile = state.getUsageRecordLogFile();
-               if (logfile == null)
-                       logfile = this.logFile;
-               if (logfile != null) {
-                       logfile = contextualizer.contextualize(logfile);
-                       synchronized (lock) {
-                               if (!logfile.equals(logDestination)) {
-                                       if (writer != null) {
-                                               writer.close();
-                                               writer = null;
-                                       }
-                                       try {
-                                               writer = new PrintWriter(new 
FileWriter(logfile));
-                                               logDestination = logfile;
-                                       } catch (IOException e) {
-                                               log.warn("failed to open usage 
record log file", e);
-                                       }
-                               }
-                               if (writer != null) {
-                                       writer.println(usageRecord);
-                                       writer.flush();
-                               }
-                       }
-               }
-
-               if (!disableDB)
-                       saveURtoDB(usageRecord);
-       }
-
-       /**
-        * How to save a usage record to the database.
-        * 
-        * @param usageRecord
-        *            The serialized usage record to save.
-        */
-       protected void saveURtoDB(String usageRecord) {
-               UsageRecord ur;
-               try {
-                       ur = new UsageRecord(usageRecord);
-               } catch (JAXBException e) {
-                       log.warn("failed to deserialize usage record", e);
-                       return;
-               }
-
-               try {
-                       self.saveURtoDB(ur);
-               } catch (RuntimeException e) {
-                       log.warn("failed to save UR to database", e);
-               }
-       }
-
-       @WithinSingleTransaction
-       public void saveURtoDB(UsageRecord ur) {
-               persist(ur);
-       }
-
-       @WithinSingleTransaction
-       public List<JobUsageRecord> getUsageRecords() {
-               @SuppressWarnings("unchecked")
-               Collection<String> urs = (Collection<String>) 
namedQuery("allByDate")
-                               .execute();
-               List<JobUsageRecord> result = new ArrayList<>();
-               for (String ur : urs)
-                       try {
-                               result.add(JobUsageRecord.unmarshal(ur));
-                       } catch (JAXBException e) {
-                               log.warn("failed to unmarshal UR", e);
-                       }
-               return result;
-       }
-
-       @PreDestroy
-       public void close() {
-               if (writer != null)
-                       writer.close();
-       }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-webapp/src/main/java/org/taverna/server/master/usage/package-info.java
----------------------------------------------------------------------
diff --git 
a/server-webapp/src/main/java/org/taverna/server/master/usage/package-info.java 
b/server-webapp/src/main/java/org/taverna/server/master/usage/package-info.java
deleted file mode 100644
index 13e14cd..0000000
--- 
a/server-webapp/src/main/java/org/taverna/server/master/usage/package-info.java
+++ /dev/null
@@ -1,9 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- * 
- * See the file "LICENSE" for license terms.
- */
-/**
- * Resource usage recording mechanism.
- */
-package org.taverna.server.master.usage;

http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-webapp/src/main/java/org/taverna/server/master/utils/CallTimeLogger.java
----------------------------------------------------------------------
diff --git 
a/server-webapp/src/main/java/org/taverna/server/master/utils/CallTimeLogger.java
 
b/server-webapp/src/main/java/org/taverna/server/master/utils/CallTimeLogger.java
deleted file mode 100644
index a1ac04a..0000000
--- 
a/server-webapp/src/main/java/org/taverna/server/master/utils/CallTimeLogger.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- * 
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import static java.lang.String.format;
-import static java.lang.System.nanoTime;
-import static java.lang.annotation.ElementType.METHOD;
-import static java.lang.annotation.RetentionPolicy.RUNTIME;
-import static org.apache.commons.logging.LogFactory.getLog;
-import static org.taverna.server.master.TavernaServer.JMX_ROOT;
-
-import java.lang.annotation.Documented;
-import java.lang.annotation.Retention;
-import java.lang.annotation.Target;
-
-import org.apache.commons.logging.Log;
-import org.aspectj.lang.ProceedingJoinPoint;
-import org.aspectj.lang.annotation.Around;
-import org.aspectj.lang.annotation.Aspect;
-import org.springframework.jmx.export.annotation.ManagedAttribute;
-import org.springframework.jmx.export.annotation.ManagedResource;
-import org.taverna.server.master.common.version.Version;
-
-/**
- * This class is responsible for timing all invocations of publicly-exposed
- * methods of the webapp. It's connected to the webapp through an AspectJ-style
- * pointcut that targets a custom annotation.
- * 
- * @author Donal Fellows
- */
-@Aspect
-@ManagedResource(objectName = JMX_ROOT + "PerformanceMonitor", description = 
"The performance monitor for Taverna Server "
-               + Version.JAVA
-               + ". Writes to application log using the category 
'Taverna.Server.Performance'.")
-public class CallTimeLogger {
-       private long threshold = 4000000;
-       private Log log = getLog("Taverna.Server.Performance");
-
-       @ManagedAttribute(description = "Threshold beneath which monitored call 
times are not logged. In nanoseconds.")
-       public long getThreshold() {
-               return threshold;
-       }
-
-       @ManagedAttribute(description = "Threshold beneath which monitored call 
times are not logged. In nanoseconds.")
-       public void setThreshold(long threshold) {
-               this.threshold = threshold;
-       }
-
-       /**
-        * The timer for this aspect. The wrapped invocation will be timed, and 
a
-        * log message written if the configured threshold is exceeded.
-        * 
-        * @param call
-        *            The call being wrapped.
-        * @return The result of the call.
-        * @throws Throwable
-        *             If anything goes wrong with the wrapped call.
-        * @see System#nanoTime()
-        */
-       
@Around("@annotation(org.taverna.server.master.utils.CallTimeLogger.PerfLogged)")
-       public Object time(ProceedingJoinPoint call) throws Throwable {
-               long fore = nanoTime();
-               try {
-                       return call.proceed();
-               } finally {
-                       long aft = nanoTime();
-                       long elapsed = aft - fore;
-                       if (elapsed > threshold)
-                               log.info(format("call to %s took %.3fms", 
call.toShortString(),
-                                               elapsed / 1000000.0));
-               }
-       }
-
-       /**
-        * Mark methods that should be counted by the invocation counter.
-        * 
-        * @author Donal Fellows
-        */
-       @Retention(RUNTIME)
-       @Documented
-       @Target(METHOD)
-       public static @interface PerfLogged {
-       }
-}

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