net.sf.taverna.t2.provenance.lineageservice
Class ProvenanceWriter

java.lang.Object
  net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter

Direct Known Subclasses:

RDFProvenanceWriter

public abstract class ProvenanceWriter
extends java.lang.Object

Handles all the writing out of provenance items to the database layer. Uses standard SQL so all specific instances of this class can extend this writer to handle all of the db writes

Author:

Paolo Missier, Ian Dunlop, Stuart Owen

Field Summary

protected int	cnt
protected static org.apache.log4j.Logger	logger
protected ProvenanceQuery	pq

Constructor Summary

ProvenanceWriter()

Method Summary

void	addArc(java.lang.String sourceVarName, java.lang.String sourceProcName, java.lang.String sinkVarName, java.lang.String sinkProcName, java.lang.String wfId)
void	addArc(Var sourceVar, Var sinkVar, java.lang.String wfId) inserts one row into the ARC DB table -- OBSOLETE, see instead
java.lang.String	addCollection(java.lang.String processorId, java.lang.String collId, java.lang.String parentCollectionId, java.lang.String iteration, java.lang.String portName, java.lang.String dataflowId)
void	addData(java.lang.String dataRef, java.lang.String wfInstanceId, byte[] data) adds (dataRef, data) pairs to the Data table (only for string data)
void	addData(java.lang.String dataRef, java.lang.String wfInstanceId, java.lang.Object data)
void	addProcessor(java.lang.String name, java.lang.String wfID, boolean isTopLevel) insert new processor into the provenance DB
void	addProcessor(java.lang.String name, java.lang.String type, java.lang.String wfNameRef, boolean isTopLevel) add a processor to the static portion of the DB with given name, type and wfnameRef scope
void	addProcessorBinding(ProcBinding pb)
void	addVarBinding(VarBinding vb)
void	addVariables(java.util.List<Var> vars, java.lang.String wfId) add each Var as a row into the VAR DB table note: no static var type available as part of the dataflow...
void	addWFId(java.lang.String wfId)
void	addWFId(java.lang.String wfId, java.lang.String parentWFname, java.lang.String externalName, java.sql.Blob dataflow)
void	addWFInstanceId(java.lang.String wfId, java.lang.String wfInstanceId)
java.util.Set<java.lang.String>	clearDBDynamic()
java.util.Set<java.lang.String>	clearDBDynamic(java.lang.String runID) deletes DB contents for all runs -- for testing purposes
void	clearDBStatic() deletes DB contents for the static structures -- called prior to each run
void	clearDBStatic(java.lang.String wfID) deletes DB contents for the static structures -- called prior to each run
void	clearDD()
abstract void	closeCurrentModel()
java.sql.Connection	getConnection()
ProvenanceQuery	getQuery()
void	replaceCollectionRecord(NestedListNode nln, java.lang.String prevPName, java.lang.String prevVarName)
void	setQuery(ProvenanceQuery query)
void	updateVar(Var v) persists var v back to DB
void	updateVarBinding(VarBinding vb)
void	writeDDRecord(java.lang.String pFrom, java.lang.String vFrom, java.lang.String valFrom, java.lang.String pTo, java.lang.String vTo, java.lang.String valTo, java.lang.String iteration, java.lang.String wfInstanceID) used to support the implementation of

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

protected static org.apache.log4j.Logger logger

cnt

protected int cnt

pq

protected ProvenanceQuery pq

Constructor Detail

ProvenanceWriter

public ProvenanceWriter()

Method Detail

getConnection

public java.sql.Connection getConnection()
                                  throws java.lang.InstantiationException,
                                         java.lang.IllegalAccessException,
                                         java.lang.ClassNotFoundException,
                                         java.sql.SQLException

Throws:

java.lang.InstantiationException

java.lang.IllegalAccessException

java.lang.ClassNotFoundException

java.sql.SQLException

closeCurrentModel

public abstract void closeCurrentModel()

addVariables

public void addVariables(java.util.List<Var> vars,
                         java.lang.String wfId)
                  throws java.sql.SQLException

add each Var as a row into the VAR DB table
note: no static var type available as part of the dataflow...

Parameters:

vars -

wfId -

Throws:

java.sql.SQLException

addArc

public void addArc(Var sourceVar,
                   Var sinkVar,
                   java.lang.String wfId)
            throws java.sql.SQLException

inserts one row into the ARC DB table -- OBSOLETE, see instead

Parameters:

sourceVar -

sinkVar -

wfId -

Throws:

java.sql.SQLException

addArc

public void addArc(java.lang.String sourceVarName,
                   java.lang.String sourceProcName,
                   java.lang.String sinkVarName,
                   java.lang.String sinkProcName,
                   java.lang.String wfId)

addWFId

public void addWFId(java.lang.String wfId)
             throws java.sql.SQLException

Throws:

java.sql.SQLException

addWFId

public void addWFId(java.lang.String wfId,
                    java.lang.String parentWFname,
                    java.lang.String externalName,
                    java.sql.Blob dataflow)
             throws java.sql.SQLException

Throws:

java.sql.SQLException

addWFInstanceId

public void addWFInstanceId(java.lang.String wfId,
                            java.lang.String wfInstanceId)
                     throws java.sql.SQLException

Throws:

java.sql.SQLException

addProcessor

public void addProcessor(java.lang.String name,
                         java.lang.String wfID,
                         boolean isTopLevel)
                  throws java.sql.SQLException

insert new processor into the provenance DB

Parameters:

name -

Throws:

java.sql.SQLException

addProcessor

public void addProcessor(java.lang.String name,
                         java.lang.String type,
                         java.lang.String wfNameRef,
                         boolean isTopLevel)
                  throws java.sql.SQLException

add a processor to the static portion of the DB with given name, type and wfnameRef scope

Parameters:

name -

type -

wfNameRef -

Throws:

java.sql.SQLException

addProcessorBinding

public void addProcessorBinding(ProcBinding pb)
                         throws java.sql.SQLException

Throws:

java.sql.SQLException

addCollection

public java.lang.String addCollection(java.lang.String processorId,
                                      java.lang.String collId,
                                      java.lang.String parentCollectionId,
                                      java.lang.String iteration,
                                      java.lang.String portName,
                                      java.lang.String dataflowId)
                               throws java.sql.SQLException

Throws:

java.sql.SQLException

addData

public void addData(java.lang.String dataRef,
                    java.lang.String wfInstanceId,
                    java.lang.Object data)
             throws java.sql.SQLException

Throws:

java.sql.SQLException

addData

public void addData(java.lang.String dataRef,
                    java.lang.String wfInstanceId,
                    byte[] data)
             throws java.sql.SQLException

adds (dataRef, data) pairs to the Data table (only for string data)

Throws:

java.sql.SQLException

addVarBinding

public void addVarBinding(VarBinding vb)
                   throws java.sql.SQLException

Parameters:

dataRef -

wfInstanceId -

data - the data in bytearray form, untyped

dve - an instance of a DataExtractor. This maps the data bytearray to a string according to the semantics of the data prior to inserting the data into the DB. It's a bit of a hack used in this impl. to extract significant parts of an XMLEncoded bean that can be then used in other contexts (mainly, in OPM graphs, where a raw byte array would not be interpreted).

Throws:

java.sql.SQLException

updateVar

public void updateVar(Var v)
               throws java.sql.SQLException

persists var v back to DB

Parameters:

v -

Throws:

java.sql.SQLException

updateVarBinding

public void updateVarBinding(VarBinding vb)

replaceCollectionRecord

public void replaceCollectionRecord(NestedListNode nln,
                                    java.lang.String prevPName,
                                    java.lang.String prevVarName)

clearDBStatic

public void clearDBStatic()
                   throws java.sql.SQLException

deletes DB contents for the static structures -- called prior to each run

Throws:

java.sql.SQLException

clearDBStatic

public void clearDBStatic(java.lang.String wfID)
                   throws java.sql.SQLException

deletes DB contents for the static structures -- called prior to each run

Throws:

java.sql.SQLException

clearDBDynamic

public java.util.Set<java.lang.String> clearDBDynamic()
                                               throws java.sql.SQLException

Throws:

java.sql.SQLException

clearDBDynamic

public java.util.Set<java.lang.String> clearDBDynamic(java.lang.String runID)
                                               throws java.sql.SQLException

deletes DB contents for all runs -- for testing purposes

Throws:

java.sql.SQLException

clearDD

public void clearDD()

writeDDRecord

public void writeDDRecord(java.lang.String pFrom,
                          java.lang.String vFrom,
                          java.lang.String valFrom,
                          java.lang.String pTo,
                          java.lang.String vTo,
                          java.lang.String valTo,
                          java.lang.String iteration,
                          java.lang.String wfInstanceID)

used to support the implementation of

Parameters:

pname -

vFrom -

valFrom -

vTo -

valTo -

iteration -

wfInstanceID -

setQuery

public void setQuery(ProvenanceQuery query)

getQuery

public ProvenanceQuery getQuery()