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LogBook Web Service

A web service wrapper for the metadata and data services used by Taverna's LogBook.

Installation

logbook-service.png

  • By default the service is configured to point at sandbox metadata and data databases. Edit the file logbook-service.properties in the webapps/logbook-service/WEB-INF/classes folder of Tomcat appropriately.

Source Code

Anonymous CVS:
  • Host: cvs.mygrid.info
  • Path: /usr/local/cvs/mygrid
  • Module: logbook-service

API

Method Summary
 void addQuad(String graphName, String subject, String predicate, String object)


          Stores the quad of arguments
 String[] getAllNestedRuns()


          Gets the LSIDs of all the nested workflow runs in store.
 String[] getAllWorkflowRuns()


          Gets the LSIDs of all the workflow runs in store.
 byte[] getBytesDataItem(String dataItemLSID)


          Returns the Taverna data object corresponding to dataItemLSID as an array of bytes if that is the type of the data object, null otherwise.
 String[] getDataCollectionLSIDs(String dataCollectionLSID)


          Returns the LSIDs in dataCollectionLSID.
 byte[] getDataItem(String dataItemLSID)


          Returns the Taverna data object corresponding to dataItemLSID as an array of bytes, even if it is a string.
 String[] getDataPortNames(String dataURN)


          Returns the names of the Taverna (input and output) ports where dataURN has passed through.
 String[] getDataSyntacticTypes(String dataLSID)


          Returns the declared syntactic types for the ports dataLSID has passed through.
 String[] getDatatypePropertyValues(String sourceIndividual, String datatypeProperty)


          Gets the array of (String representations of) the targets of datatypeProperty for sourceIndividual.
 String getFirstDatatypePropertyValue(String sourceIndividual, String datatypeProperty)


          Gets the first String value of datatypeProperty for sourceIndividual.
 String getFirstObjectPropertyValue(String sourceIndividual, String objectProperty)


          Gets the String representation of the first target of objectProperty for sourceIndividual.
 String[] getIndividualsOfType(String type)


          Returns all the individuals of type.
 String[] getInputDataPortNames(String dataURN)


          Returns the names of the Taverna input ports where dataURN has passed through.
 String[] getNestedRuns(String workflowRunId)


          Gets the names of the nested workflow runs for workflowRun.
 String[] getNonNestedProcessRuns(String workflowRunId)


          Gets all the (ids of) process runs executed by workflowRunLSID that are not nested workflows.
 String[] getObjectPropertyValues(String sourceIndividual, String objectProperty)


          Gets the array of (String representations of) the targets of objectProperty for sourceIndividual.
 String[] getOutputDataPortNames(String dataURN)


          Returns the names of the Taverna output ports where dataURN has passed through.
 String[] getProcessInputs(String processID)


          Gets all the (ids of) inputs for processID
 String[] getProcessOutputs(String processID)


          Gets all the (ids of) outputs for processID
 String[] getProcessRuns(String workflowRunId)


          Gets all the (ids of) process runs executed by workflowRunLSID

 String

 getStringDataItem(String dataItemLSID)


          Returns the Taverna data object corresponding to dataItemLSID as a String if that is the type of the data object, null otherwise.
 String getUnparsedProcessEndDate(String processRun)


          Returns the end date of processRun.

 String

 getUnparsedWorkflowStartDate(String workflowRun)


          Returns the start date of workflowRun.
 String[] getUserWorkFlows(String experimenter)


          Returns the LSIDs of all the runs executed by experimenter.
 String getWorkflow(String workflowLSID)


          Returns the Scufl workflow (as an XML string) with (dynamically assigned) LSID workflowLSID.
 String getWorkflowExecutedByRun(String workflowRun)


          Returns the Scufl workflow (as an XML string) that was executed in workflowRun
 String[] getWorkflowInputs(String lsid)


          Gets all the (ids of) workflow inputs for workflowRunLSID
 String[] getWorkflowOutputs(String workflowRunLSID)


          Gets all the (ids of) workflow outputs for workflowRunLSID

 String

 getWorkflowRun(String workflowRunId)


          Retrieves the graph corresponding to workflowRunId together with all the subgraphs of processes and nested runs and returns it as a String containing its RDF/XML representation.

 boolean

 isIndividualOfType(String individual, String type)


          Returns true if individual is of type type.
 boolean isProcessIteration(String processURI)


          Returns true if processURI is an iteration run.
 boolean isProcessWithIterations(String processURI)


          Returns true if processURI contains iterations.
 void removeGraph(String graphName)


          Removes the graph graphName.
 void removeWorkflowRun(String workflowRun)


          Removes the graph corresponding to workflowRun from the repository and then does the same by recursion for all its possible nested workflow runs and process runs.

 String

 retrieveGraph(String workflowRunId)


          Retrieves the graph corresponding to graphName and returns it as a String containing its RDF/XML representation.
 void storeModelFromURL(String url, String graphName)


          Stores under graphName the RDF graph corresponding to the OWL ontology at url.

 void

 storeRDFGraph(String rdfGraph, String graphName)


          Stores rdfGraph under graphName.
 
Methods inherited from class Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

getWorkflowExecutedByRun

public String getWorkflowExecutedByRun(String workflowRun)

Returns the Scufl workflow (as an XML string) that was executed in workflowRun

Parameters:
workflowRun - the LSID of a workflow run.
Returns:
a String
See Also:
getWorkflow(String)

getWorkflow

public String getWorkflow(String workflowLSID)
Returns the Scufl workflow (as an XML string) with (dynamically assigned) LSID workflowLSID. Note that workflowLSID

is not the declared LSID for the workflow, but rather the one dynamically assigned by the LogBook during its execution in Taverna.

Parameters:
workflowLSID -
Returns:
a String
See Also:
getWorkflowExecutedByRun(String)

getDataItem

public byte[] getDataItem(String dataItemLSID)
Returns the Taverna data object corresponding to dataItemLSID as an array of bytes, even if it is a string.

Parameters:
dataItemLSID -

Returns:
byte[]

getBytesDataItem

public byte[] getBytesDataItem(String dataItemLSID)

Returns the Taverna data object corresponding to dataItemLSID as an array of bytes if that is the type of the data object, null otherwise.

Parameters:
dataItemLSID -
Returns:
byte[]

getStringDataItem

public String getStringDataItem(String dataItemLSID)
Returns the Taverna data object corresponding to dataItemLSID as a String if that is the type of the data object, null otherwise.

Parameters:
dataItemLSID -
Returns:
String

getDataPortNames


public String[] getDataPortNames(String dataURN)
Returns the names of the Taverna (input and output) ports where dataURN has passed through.

Parameters:
dataURN -
Returns:
an array of Strings

getInputDataPortNames

public String[] getInputDataPortNames(String dataURN)
Returns the names of the Taverna input ports where dataURN

has passed through.

Parameters:
dataURN -
Returns:
an array of Strings

getOutputDataPortNames

public String[] getOutputDataPortNames(String dataURN)
Returns the names of the Taverna output ports where dataURN has passed through.

Parameters:
dataURN -

Returns:
an array of Strings

getDataCollectionLSIDs

public String[] getDataCollectionLSIDs(String dataCollectionLSID)

Returns the LSIDs in dataCollectionLSID.

Parameters:
dataCollectionLSID -
Returns:
an array of Strings

getDataSyntacticTypes

public String[] getDataSyntacticTypes(String dataLSID)
Returns the declared syntactic types for the ports dataLSID has passed through.

Parameters:
dataLSID -

Returns:
an array of Strings

storeRDFGraph

public void storeRDFGraph(String rdfGraph,
                          String graphName)

Stores rdfGraph under graphName. Note that if a graph with the same name already exists it will be replaced with the new one.

Parameters:
rdfGraph - a String consisting of (an XML serialization of) an RDF graph.
graphName - a String.

storeModelFromURL

public void storeModelFromURL(String url,
                              String graphName)
Stores under graphName the RDF graph corresponding to the OWL ontology at url. Note that if a graph with the same name already exists it will be replaced with the new one.

Parameters:
url - a URL pointing to an OWL ontology.
graphName - a String.

addQuad

public void addQuad(String graphName,
                    String subject,
                    String predicate,
                    String object)
Stores the quad of arguments

Parameters:
graphName -
subject -
predicate -
object -

retrieveGraph

public String retrieveGraph(String workflowRunId)
Retrieves the graph corresponding to graphName and returns it as a String containing its RDF/XML representation.

Parameters:
workflowRunId - a String.
Returns:
a String containing (an XML serialization of) an RDF representation of the graph.

removeGraph


public void removeGraph(String graphName)
Removes the graph graphName.

Parameters:
graphName - the name of the graph to be removed.

removeWorkflowRun

public void removeWorkflowRun(String workflowRun)
Removes the graph corresponding to workflowRun from the repository and then does the same by recursion for all its possible nested workflow runs and process runs.

Parameters:
workflowRun -

getWorkflowRun

public String getWorkflowRun(String workflowRunId)

Retrieves the graph corresponding to workflowRunId together with all the subgraphs of processes and nested runs and returns it as a String containing its RDF/XML representation.

Parameters:
workflowRunId - a String.
Returns:
a String containing an RDF/XML representation of the graph.

getAllWorkflowRuns

public String[] getAllWorkflowRuns()
Gets the LSIDs of all the workflow runs in store.

Returns:
an array of Strings

getProcessRuns

public String[] getProcessRuns(String workflowRunId)

Gets all the (ids of) process runs executed by workflowRunLSID

Parameters:
workflowRunId -
Returns:
an array of Strings
See Also:
getNonNestedProcessRuns(String)

getNestedRuns

public String[] getNestedRuns(String workflowRunId)
Gets the names of the nested workflow runs for workflowRun.

Parameters:
workflowRunId -
Returns:
an array of Strings

getAllNestedRuns

public String[] getAllNestedRuns()

Gets the LSIDs of all the nested workflow runs in store.

Returns:
a List of Strings

getNonNestedProcessRuns

public String[] getNonNestedProcessRuns(String workflowRunId)
Gets all the (ids of) process runs executed by workflowRunLSID that are not nested workflows.

Parameters:
workflowRunId -

Returns:
an array of Strings
See Also:
getProcessRuns(String)

getWorkflowInputs

public String[] getWorkflowInputs(String lsid)

Gets all the (ids of) workflow inputs for workflowRunLSID

Parameters:
lsid -
Returns:
an array of Strings

getWorkflowOutputs

public String[] getWorkflowOutputs(String workflowRunLSID)
Gets all the (ids of) workflow outputs for workflowRunLSID

Parameters:
workflowRunLSID -

Returns:
an array of Strings

getProcessOutputs

public String[] getProcessOutputs(String processID)

Gets all the (ids of) outputs for processID

Parameters:
processID -
Returns:
an array of Strings

getProcessInputs

public String[] getProcessInputs(String processID)
Gets all the (ids of) inputs for processID

Parameters:
processID -

Returns:
an array of Strings

getUserWorkFlows

public String[] getUserWorkFlows(String experimenter)

Returns the LSIDs of all the runs executed by experimenter. Note that the experimenter for a run is set by default to http://www.someplace/someuser.

Parameters:
experimenter -
Returns:
an array of Strings

isProcessIteration

public boolean isProcessIteration(String processURI)
Returns true if processURI is an iteration run.

Parameters:
processURI -
Returns:
a boolean

isProcessWithIterations


public boolean isProcessWithIterations(String processURI)
Returns true if processURI contains iterations.

Parameters:
processURI -

Returns:
a boolean

getUnparsedWorkflowStartDate

public String getUnparsedWorkflowStartDate(String workflowRun)

Returns the start date of workflowRun.

Parameters:
workflowRun -
Returns:
a String

getUnparsedProcessEndDate

public String getUnparsedProcessEndDate(String processRun)
Returns the end date of processRun.

Parameters:
processRun -

Returns:
a String

getObjectPropertyValues

public String[] getObjectPropertyValues(String sourceIndividual,
                                                  String objectProperty)

Gets the array of (String representations of) the targets of objectProperty for sourceIndividual.

Parameters:
sourceIndividual - String
objectProperty - String
Returns:
an array of Strings

getFirstObjectPropertyValue

public String getFirstObjectPropertyValue(String sourceIndividual,
                                                    String objectProperty)
Gets the String representation of the first target of objectProperty for sourceIndividual.

Parameters:
sourceIndividual - String
objectProperty - String
Returns:
String

getDatatypePropertyValues

public String[] getDatatypePropertyValues(String sourceIndividual,
                                                    String datatypeProperty)
Gets the array of (String representations of) the targets of datatypeProperty for sourceIndividual.

Parameters:
sourceIndividual - String
datatypeProperty - String
Returns:
an array of Strings

getFirstDatatypePropertyValue

public String getFirstDatatypePropertyValue(String sourceIndividual,
                                                      String datatypeProperty)
Gets the first String value of datatypeProperty for sourceIndividual.

Parameters:
sourceIndividual - String
datatypeProperty - String

Returns:
String

getIndividualsOfType

public String[] getIndividualsOfType(String type)

Returns all the individuals of type.

Parameters:
type -
Returns:
a List of Strings.

isIndividualOfType

public boolean isIndividualOfType(String individual,
                                  String type)
Returns true if individual is of type type.

Parameters:
individual -
type -
Returns:
a boolean

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pngpng logbook-service.png manage 146.8 K 19 Feb 2007 - 16:22 DanieleTuri Screenshot of available services
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