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Posted to commits@taverna.apache.org by re...@apache.org on 2015/03/30 15:47:20 UTC
[08/12] incubator-taverna-engine git commit: some provenance
refactoring
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/ProvenanceWriter.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/ProvenanceWriter.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/ProvenanceWriter.java
deleted file mode 100644
index 23ad705..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/ProvenanceWriter.java
+++ /dev/null
@@ -1,676 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice;
-
-import static net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector.DataflowInvocationTable.DataflowInvocation;
-
-import java.sql.Blob;
-import java.sql.Connection;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.sql.Statement;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.UUID;
-
-import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector.ActivityTable;
-import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector.DataBindingTable;
-import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector.DataflowInvocationTable;
-import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector.ProcessorEnactmentTable;
-import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector.ServiceInvocationTable;
-import net.sf.taverna.t2.provenance.lineageservice.utils.NestedListNode;
-import net.sf.taverna.t2.provenance.lineageservice.utils.Port;
-import net.sf.taverna.t2.provenance.lineageservice.utils.PortBinding;
-import net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceProcessor;
-
-import org.apache.log4j.Logger;
-
-import uk.org.taverna.configuration.database.DatabaseManager;
-
-/**
- * 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
- * @author Ian Dunlop
- * @author Stuart Owen
- *
- */
-public class ProvenanceWriter {
-
- protected static Logger logger = Logger.getLogger(ProvenanceWriter.class);
- protected int cnt; // counts number of calls to PortBinding
- protected ProvenanceQuery pq = null;
- private final DatabaseManager databaseManager;
-
- public ProvenanceWriter(DatabaseManager databaseManager) {
- this.databaseManager = databaseManager;
- }
-
- public Connection getConnection() throws SQLException {
- return databaseManager.getConnection();
- }
-
- public void closeCurrentModel() {
-
- }
-
- /**
- * add each Port as a row into the Port DB table <strong>note: no static
- * port type available as part of the dataflow...</strong>
- *
- * @param ports
- * @param wfId
- * @throws SQLException
- */
- public void addPorts(List<Port> ports, String wfId) throws SQLException {
- String sql = "INSERT INTO Port "
- + "(portName, processorName, isInputPort, depth, workflowId, portId, processorId)"
- + " VALUES(?,?,?,?,?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- for (Port v : ports) {
- ps.setString(1, v.getPortName());
- ps.setString(2, v.getProcessorName());
- ps.setBoolean(3, v.isInputPort());
- int depth = v.getDepth() >= 0 ? v.getDepth() : 0;
- ps.setInt(4, depth);
- ps.setString(5, wfId);
- ps.setString(6, v.getIdentifier());
- ps.setString(7, v.getProcessorId());
-
- try {
- ps.executeUpdate();
- } catch (Exception e) {
- logger.warn("Could not insert var " + v.getPortName(), e);
- }
- }
- }
- }
-
- @SuppressWarnings("static-access")
- public void addDataflowInvocation(
- net.sf.taverna.t2.provenance.lineageservice.utils.DataflowInvocation invocation)
- throws SQLException {
- String sql = "INSERT INTO " + DataflowInvocation.DataflowInvocation
- + "(" + DataflowInvocation.dataflowInvocationId + ","
- + DataflowInvocation.workflowId + ","
- + DataflowInvocation.invocationStarted + ","
- + DataflowInvocation.invocationEnded + ","
- + DataflowInvocation.inputsDataBinding + ","
- + DataflowInvocation.outputsDataBinding + ","
- + DataflowInvocation.parentProcessorEnactmentId + ","
- + DataflowInvocation.workflowRunId + ","
- + DataflowInvocation.completed + ") "
- + " VALUES(?,?,?,?,?,?,?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql);) {
- ps.setString(1, invocation.getDataflowInvocationId());
- ps.setString(2, invocation.getWorkflowId());
- ps.setTimestamp(3, invocation.getInvocationStarted());
- ps.setTimestamp(4, invocation.getInvocationEnded());
- ps.setString(5, invocation.getInputsDataBindingId());
- ps.setString(6, invocation.getOutputsDataBindingId());
- ps.setString(7, invocation.getParentProcessorEnactmentId());
- ps.setString(8, invocation.getWorkflowRunId());
- ps.setBoolean(9, invocation.getCompleted());
-
- ps.executeUpdate();
- }
- }
-
- /**
- * inserts one row into the ARC DB table
- *
- * @param sourcePort
- * @param destinationPort
- * @param workflowId
- */
- public void addDataLink(Port sourcePort, Port destinationPort,
- String workflowId) throws SQLException {
- String sql = "INSERT INTO Datalink (workflowId, sourceProcessorName, "
- + " sourcePortName, destinationProcessorName, destinationPortName,"
- + " sourcePortId, destinationPortId) "
- + "VALUES(?,?,?,?,?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, workflowId);
- ps.setString(2, sourcePort.getProcessorName());
- ps.setString(3, sourcePort.getPortName());
- ps.setString(4, destinationPort.getProcessorName());
- ps.setString(5, destinationPort.getPortName());
- ps.setString(6, sourcePort.getIdentifier());
- ps.setString(7, destinationPort.getIdentifier());
-
- ps.executeUpdate();
- }
- }
-
- public void addDataBinding(
- net.sf.taverna.t2.provenance.lineageservice.utils.DataBinding dataBinding)
- throws SQLException {
- String sql = "INSERT INTO " + DataBindingTable.DataBinding + "("
- + DataBindingTable.dataBindingId + ","
- + DataBindingTable.portId + "," + DataBindingTable.t2Reference
- + "," + DataBindingTable.workflowRunId + ") VALUES(?,?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, dataBinding.getDataBindingId());
- ps.setString(2, dataBinding.getPort().getIdentifier());
- ps.setString(3, dataBinding.getT2Reference());
- ps.setString(4, dataBinding.getWorkflowRunId());
- ps.executeUpdate();
- if (logger.isDebugEnabled())
- logger.debug("adding DataBinding:\n " + dataBinding);
- }
- }
-
- public void addWFId(String wfId) throws SQLException {
- String sql = "INSERT INTO Workflow (workflowId) VALUES (?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, wfId);
- ps.executeUpdate();
- }
- }
-
- public void addWFId(String wfId, String parentWorkflowId,
- String externalName, Blob dataflow) throws SQLException {
- String sql = "INSERT INTO Workflow (workflowId, parentWorkflowId, externalName, dataflow) "
- + "VALUES (?, ?, ?, ?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, wfId);
- ps.setString(2, parentWorkflowId);
- ps.setString(3, externalName);
- ps.setBlob(4, dataflow);
-
- ps.executeUpdate();
- }
- }
-
- public void addWorkflowRun(String wfId, String workflowRunId)
- throws SQLException {
- String sql = "INSERT INTO WorkflowRun (workflowRunId, workflowId) VALUES (?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, workflowRunId);
- ps.setString(2, wfId);
-
- ps.executeUpdate();
- }
- }
-
- /**
- * insert new processor into the provenance DB
- *
- * @param name
- * @throws SQLException
- */
- public ProvenanceProcessor addProcessor(String name, String wfID,
- boolean isTopLevel) throws SQLException {
- ProvenanceProcessor provProc = new ProvenanceProcessor();
- provProc.setIdentifier(UUID.randomUUID().toString());
- provProc.setProcessorName(name);
- provProc.setWorkflowId(wfID);
- provProc.setTopLevelProcessor(isTopLevel);
- // pType is unknown
- addProcessor(provProc);
- return provProc;
- }
-
- /**
- * add a processor to the static portion of the DB with given name, type and
- * workflowId scope
- *
- * @param name
- * @param type
- * @param workflowId
- * @throws SQLException
- */
- public void addProcessor(ProvenanceProcessor provProc) throws SQLException {
- String sql = "INSERT INTO Processor (processorName, firstActivityClass, workflowId, isTopLevel, processorId) "
- + "VALUES (?,?,?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql);) {
- ps.setString(1, provProc.getProcessorName());
- ps.setString(2, provProc.getFirstActivityClassName());
- ps.setString(3, provProc.getWorkflowId());
- ps.setBoolean(4, provProc.isTopLevelProcessor());
- ps.setString(5, provProc.getIdentifier());
-
- ps.executeUpdate();
- }
- }
-
- public void addProcessorEnactment(
- net.sf.taverna.t2.provenance.lineageservice.utils.ProcessorEnactment enactment)
- throws SQLException {
- String sql = "INSERT INTO "
- + ProcessorEnactmentTable.ProcessorEnactment + "("
- + ProcessorEnactmentTable.processEnactmentId + ","
- + ProcessorEnactmentTable.workflowRunId + ","
- + ProcessorEnactmentTable.processorId + ","
- + ProcessorEnactmentTable.processIdentifier + ","
- + ProcessorEnactmentTable.iteration + ","
- + ProcessorEnactmentTable.parentProcessorEnactmentId + ","
- + ProcessorEnactmentTable.enactmentStarted + ","
- + ProcessorEnactmentTable.enactmentEnded + ","
- + ProcessorEnactmentTable.initialInputsDataBindingId + ","
- + ProcessorEnactmentTable.finalOutputsDataBindingId
- + ") VALUES(?,?,?,?,?,?,?,?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, enactment.getProcessEnactmentId());
- ps.setString(2, enactment.getWorkflowRunId());
- ps.setString(3, enactment.getProcessorId());
- ps.setString(4, enactment.getProcessIdentifier());
- ps.setString(5, enactment.getIteration());
- ps.setString(6, enactment.getParentProcessorEnactmentId());
- ps.setTimestamp(7, enactment.getEnactmentStarted());
- ps.setTimestamp(8, enactment.getEnactmentEnded());
- ps.setString(9, enactment.getInitialInputsDataBindingId());
- ps.setString(10, enactment.getFinalOutputsDataBindingId());
- ps.executeUpdate();
-
- if (logger.isDebugEnabled())
- logger.debug("adding ProcessorEnactment binding:\n "
- + enactment);
- }
- }
-
- public String addCollection(String processorId, String collId,
- String parentCollectionId, String iteration, String portName,
- String dataflowId) throws SQLException {
- String newParentCollectionId = null;
- String sql = "INSERT INTO Collection (processorNameRef, workflowRunId, portName, iteration, parentCollIdRef, collId) "
- + "VALUES(?, ?, ?, ?, ?, ?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- if (parentCollectionId == null)
- // this is a top-level list
- parentCollectionId = "TOP";
-
- newParentCollectionId = collId;
-
- ps.setString(1, processorId);
- ps.setString(2, dataflowId);
- ps.setString(3, portName);
- ps.setString(4, iteration);
- ps.setString(5, parentCollectionId);
- ps.setString(6, collId);
-
- ps.executeUpdate();
- }
-
- return newParentCollectionId;
- }
-
- public void addData(String dataRef, String wfInstanceId, Object data)
- throws SQLException {
- String sql = "INSERT INTO Data (dataReference,wfInstanceID,data) VALUES (?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql);) {
- ps.setString(1, dataRef);
- ps.setString(2, wfInstanceId);
- ps.setString(3, (String) data);
-
- ps.executeUpdate();
-
- cnt++;
-
- logger.debug("addData executed on data value from char: "
- + data);
- } catch (SQLException e) {
- // the same ID will come in several times -- duplications are
- // expected, don't panic
- }
- }
-
- /**
- * OBSOLETE
- * <p/>
- * adds (dataRef, data) pairs to the Data table (only for string data)
- */
- public void addData(String dataRef, String wfInstanceId, byte[] data)
- throws SQLException {
- String sql = "INSERT INTO Data (dataReference,wfInstanceID,data) VALUES (?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, dataRef);
- ps.setString(2, wfInstanceId);
- ps.setBytes(3, data);
-
- ps.executeUpdate();
-
- cnt++;
-
- logger.debug("addData executed on data value from char: " + data);
-
- } catch (SQLException e) {
- // the same ID will come in several times -- duplications are
- // expected, don't panic
- }
- }
-
- public void addPortBinding(PortBinding vb) throws SQLException {
- logger.debug("START addVarBinding proc " + vb.getProcessorName()
- + " port " + vb.getPortName());
- String sql = "INSERT INTO PortBinding (workflowId, processorNameRef, workflowRunId, portName, valueType, value, ref, collIdRef, iteration,positionInColl) "
- + "VALUES(?,?,?,?,?,?,?,?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, vb.getWorkflowId());
- ps.setString(2, vb.getProcessorName());
- ps.setString(3, vb.getWorkflowRunId());
- ps.setString(4, vb.getPortName());
- ps.setString(5, vb.getValueType());
- ps.setString(6, vb.getValue());
- ps.setString(7, vb.getReference());
- ps.setString(8, vb.getCollIDRef());
- ps.setString(9, vb.getIteration());
- ps.setInt(10, vb.getPositionInColl());
-
- logger.debug("addVarBinding query: \n" + ps.toString());
- ps.executeUpdate();
- logger.debug("insert done");
-
- logger.debug("COMPLETE addVarBinding proc " + vb.getProcessorName()
- + " port " + vb.getPortName());
-
- cnt++; // who uses this?
- }
- }
-
- /**
- * persists var v back to DB
- *
- * @param v
- * @throws SQLException
- */
- public void updatePort(Port v) throws SQLException {
- String sql = "UPDATE Port SET isInputPort=?, depth=?,"
- + "resolvedDepth=?, iterationStrategyOrder=? "
- + "WHERE portId=?";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setInt(1, v.isInputPort() ? 1 : 0);
- ps.setInt(2, v.getDepth());
- if (v.isResolvedDepthSet()) {
- ps.setInt(3, v.getResolvedDepth());
- } else {
- ps.setString(3, null);
- }
- ps.setInt(4, v.getIterationStrategyOrder());
- ps.setString(5, v.getIdentifier());
- ps.execute();
- }
- }
-
- public void updateProcessorEnactment(
- net.sf.taverna.t2.provenance.lineageservice.utils.ProcessorEnactment enactment) {
- String sql = "UPDATE " + ProcessorEnactmentTable.ProcessorEnactment
- + " SET " + ProcessorEnactmentTable.finalOutputsDataBindingId
- + "=?, " + ProcessorEnactmentTable.enactmentEnded + "=?"
- + " WHERE " + ProcessorEnactmentTable.processEnactmentId + "=?";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, enactment.getFinalOutputsDataBindingId());
- ps.setTimestamp(2, enactment.getEnactmentEnded());
- ps.setString(3, enactment.getProcessEnactmentId());
-
- ps.executeUpdate();
- } catch (SQLException e) {
- logger.warn("**** insert failed for query ", e);
- }
- }
-
- public void updatePortBinding(PortBinding vb) {
- String sql = "UPDATE PortBinding SET valueType = ?, value = ?, ref = ?, collIdRef = ?, positionInColl = ? "
- + "WHERE portName = ? AND workflowRunId = ? AND processorNameRef = ? AND iteration = ?" ;
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- // Update values
- ps.setString(1, vb.getValueType());
- ps.setString(2, vb.getValue());
- ps.setString(3, vb.getReference());
- ps.setString(4, vb.getCollIDRef());
- ps.setInt(5, vb.getPositionInColl());
- // Where clauses
- ps.setString(6, vb.getPortName());
- ps.setString(7, vb.getWorkflowRunId());
- ps.setString(8, vb.getProcessorName());
- ps.setString(9, vb.getIteration());
-
- ps.executeUpdate();
-
- cnt++;
-
- } catch (SQLException e) {
- logger.warn("**** insert failed for query ", e);
- }
- }
-
- public void replaceCollectionRecord(NestedListNode nln, String prevPName,
- String prevPortName) {
- String sql = "DELETE FROM Collection WHERE collId = ? AND workflowRunId = ?"
- + " AND portName = ? AND processorNameRef = ? AND iteration = ?";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, nln.getCollectionT2Reference());
- ps.setString(2, nln.getWorkflowRunId());
- ps.setString(3, prevPortName);
- ps.setString(4, prevPName);
- ps.setString(5, nln.getIteration());
-
- ps.executeUpdate();
- } catch (SQLException e) {
- logger.warn("Error replacing collection record", e);
- }
-
- try {
- addCollection(prevPName, nln.getCollectionT2Reference(),
- nln.getParentCollIdRef(), nln.getIteration(), prevPortName,
- nln.getWorkflowRunId());
- } catch (SQLException e) {
- logger.warn("Collection insert failed", e);
- }
- }
-
- /**
- * deletes DB contents for the static structures -- called prior to each run
- *
- * @throws SQLException
- */
- public void clearDBStatic() throws SQLException {
- try (Connection connection = getConnection();
- Statement stmt = connection.createStatement()) {
- stmt.executeUpdate("DELETE FROM Workflow");
- stmt.executeUpdate("DELETE FROM Processor");
- stmt.executeUpdate("DELETE FROM Datalink");
- stmt.executeUpdate("DELETE FROM Port");
- stmt.executeUpdate("DELETE FROM " + ActivityTable.Activity);
- logger.info("DB cleared STATIC");
- } catch (SQLException e) {
- logger.warn("Could not clear static database", e);
- }
- }
-
- /**
- * deletes DB contents for the static structures -- called prior to each run
- *
- * @throws SQLException
- */
- public void clearDBStatic(String wfID) throws SQLException {
- try (Connection connection = getConnection()) {
- try (PreparedStatement ps = connection
- .prepareStatement("DELETE FROM Workflow WHERE workflowId = ?")) {
- ps.setString(1, wfID);
- ps.executeUpdate();
- }
- try (PreparedStatement ps = connection
- .prepareStatement("DELETE FROM Processor WHERE workflowId = ?")) {
- ps.setString(1, wfID);
- ps.executeUpdate();
- }
- try (PreparedStatement ps = connection
- .prepareStatement("DELETE FROM Datalink WHERE workflowId = ?")) {
- ps.setString(1, wfID);
- ps.executeUpdate();
- }
- try (PreparedStatement ps = connection
- .prepareStatement("DELETE FROM Port WHERE workflowId = ?")) {
- ps.setString(1, wfID);
- ps.executeUpdate();
- }
- try (PreparedStatement ps = connection
- .prepareStatement("DELETE FROM " + ActivityTable.Activity
- + " WHERE " + ActivityTable.workflowId + "=?")) {
- ps.setString(1, wfID);
- ps.executeUpdate();
- }
- }
- logger.info("DB cleared STATICfor wfID " + wfID);
- }
-
- public Set<String> clearDBDynamic() throws SQLException {
- return clearDBDynamic(null);
- }
-
- private void delete(Connection connection, Object table, String runID) throws SQLException {
- if (runID != null) {
- try (PreparedStatement ps = connection
- .prepareStatement("DELETE FROM " + table
- + " WHERE workflowRunId = ?")) {
- ps.setString(1, runID);
- ps.executeUpdate();
- }
- } else
- try (PreparedStatement ps = connection
- .prepareStatement("DELETE FROM " + table)) {
- ps.executeUpdate();
- }
- }
- /**
- * deletes DB contents for all runs -- for testing purposes
- *
- * @throws SQLException
- */
- public Set<String> clearDBDynamic(String runID) throws SQLException {
- Set<String> refsToRemove = collectValueReferences(runID);
- // collect all relevant refs from PortBinding and Collection
-
- try (Connection connection = getConnection()) {
- delete(connection, "WorkflowRun", runID);
- delete(connection, "PortBinding", runID);
- delete(connection, "Collection", runID);
- delete(connection, DataflowInvocationTable.DataflowInvocation, runID);
- delete(connection, ServiceInvocationTable.ServiceInvocation, runID);
- delete(connection, ProcessorEnactmentTable.ProcessorEnactment, runID);
- delete(connection, DataBindingTable.DataBinding, runID);
- }
- logger.info("DB cleared DYNAMIC");
- return refsToRemove;
- }
-
- private Set<String> collectValueReferences(String runID)
- throws SQLException {
- Set<String> refs = new HashSet<>();
- try (Connection connection = getConnection()) {
- String sql = "SELECT value FROM PortBinding";
- if (runID != null)
- sql += " WHERE workflowRunId = ?";
- try (PreparedStatement ps = connection.prepareStatement(sql)) {
- if (runID != null)
- ps.setString(1, runID);
- ResultSet rs = ps.executeQuery();
- while (rs.next())
- refs.add(rs.getString("value"));
- }
-
- sql = "SELECT collId FROM Collection";
- if (runID != null)
- sql += " WHERE workflowRunId = ?";
- try (PreparedStatement ps = connection.prepareStatement(sql)) {
- if (runID != null)
- ps.setString(1, runID);
- ResultSet rs = ps.executeQuery();
- while (rs.next())
- refs.add(rs.getString("collId"));
- }
- } catch (SQLException e) {
- logger.error("Problem collecting value references for: " + runID
- + " : " + e);
- }
- return refs;
- }
-
- public void clearDD() {
- try (Connection connection = getConnection();
- Statement stmt = connection.createStatement()) {
- stmt.executeUpdate("DELETE FROM DD");
- } catch (SQLException e) {
- logger.warn("Error execting delete query for provenance records", e);
- }
- }
-
- /**
- * used to support the implementation of
- *
- * @param pname
- * @param vFrom
- * @param valFrom
- * @param vTo
- * @param valTo
- * @param iteration
- * @param workflowRunId
- */
- public void writeDDRecord(String pFrom, String vFrom, String valFrom,
- String pTo, String vTo, String valTo, String iteration,
- String workflowRunId) {
- String sql = "INSERT INTO DD (PFrom,VFrom,valFrom,PTo,VTo,valTo,iteration,workflowRun) VALUES "
- + "(?,?,?,?,?,?,?)";
- try (Connection connection = getConnection();
- PreparedStatement ps = connection.prepareStatement(sql)) {
- ps.setString(1, pFrom);
- ps.setString(2, vFrom);
- ps.setString(3, valFrom);
- ps.setString(4, pTo);
- ps.setString(5, vTo);
- ps.setString(6, iteration);
- ps.setString(7, workflowRunId);
- ps.executeUpdate();
- } catch (SQLException e) {
- logger.warn("Error inserting record into DD", e);
- }
- }
-
- public void setQuery(ProvenanceQuery query) {
- this.pq = query;
- }
-
- public ProvenanceQuery getQuery() {
- return this.pq;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/URIGenerator.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/URIGenerator.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/URIGenerator.java
deleted file mode 100644
index 94a0b8a..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/URIGenerator.java
+++ /dev/null
@@ -1,58 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice;
-
-import java.net.URI;
-import java.net.URISyntaxException;
-
-public class URIGenerator {
-
- public String makeT2ReferenceURI(String collId) {
- // collId is of the form t2:list//<UUID>
- // map to a proper URI
-
- String[] tokens = collId.split("//");
- String type = tokens[0].split(":")[1];
- String namespace = tokens[1].split("/")[0].split("\\?")[0];
- String dataId = tokens[1].split("\\?")[1];
- return "http://ns.taverna.org.uk/2011/data/" + namespace + "/" + type + "/" + dataId;
- }
-
- public String makeWFInstanceURI(String workflowRunId) {
- return "http://ns.taverna.org.uk/2011/run/" + workflowRunId + "/";
- }
-
- public String makeWorkflowURI(String wfId) {
- return "http://ns.taverna.org.uk/2010/workflow/" + wfId + "/";
- }
-
- public String makePortURI(String wfId, String pName, String vName,
- boolean inputPort) {
- return makeProcessorURI(pName, wfId) + (inputPort ? "in/" : "out/")
- + escape(vName);
- }
-
- public String escape(String part) {
- try {
- return new URI(null, null, part.replace("/", "%47"), null)
- .getRawPath();
- } catch (URISyntaxException e) {
- throw new RuntimeException("Can't escape URI part " + part, e);
- }
- }
-
- public String makeProcessorURI(String pName, String wfId) {
- return makeWorkflowURI(wfId) + "processor/" + escape(pName) + "/";
- }
-
- public String makeIteration(String workflowRunId, String workflowId,
- String processorName, String iteration) {
- String iterationUri = iteration.replace(',', '-').replace('[', ' ')
- .replace(']', ' ').trim();
-
- return makeWFInstanceURI(workflowRunId) + "workflow/" + workflowId
- + "/processor/" + processorName + "/iteration/" + iterationUri;
- }
-
- public URI makeRunUri(String workflowRunId) {
- return URI.create(makeWFInstanceURI(workflowRunId));
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/WorkflowDataProcessor.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/WorkflowDataProcessor.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/WorkflowDataProcessor.java
deleted file mode 100644
index 25369fd..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/WorkflowDataProcessor.java
+++ /dev/null
@@ -1,453 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.provenance.lineageservice;
-
-import static net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceUtils.iterationToString;
-import static net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceUtils.parentProcess;
-
-import java.sql.SQLException;
-import java.sql.Timestamp;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.UUID;
-import java.util.concurrent.ConcurrentHashMap;
-
-import net.sf.taverna.t2.facade.WorkflowInstanceFacade.State;
-import net.sf.taverna.t2.provenance.item.DataflowRunComplete;
-import net.sf.taverna.t2.provenance.item.ProvenanceItem;
-import net.sf.taverna.t2.provenance.item.WorkflowDataProvenanceItem;
-import net.sf.taverna.t2.provenance.lineageservice.utils.DataBinding;
-import net.sf.taverna.t2.provenance.lineageservice.utils.DataflowInvocation;
-import net.sf.taverna.t2.provenance.lineageservice.utils.Port;
-import net.sf.taverna.t2.provenance.lineageservice.utils.PortBinding;
-import net.sf.taverna.t2.provenance.lineageservice.utils.ProcessorEnactment;
-
-import org.apache.log4j.Logger;
-
-/**
- * @author paolo
- * this class manages the outputs from a workflow, as they come along through WorkflowData events
- */
-public class WorkflowDataProcessor {
- private static Logger logger = Logger.getLogger(WorkflowDataProcessor.class);
-
- // set of trees (impl as lists), one for each portName
- // PM portName not enough must use the WFID as context as well, because the same output portName
- // may occur in multiple nested workflows
- Map<String, List<WorkflowDataNode>> workflowDataTrees = new HashMap<>();
-
- protected Map<String, Timestamp> workflowStarted = new ConcurrentHashMap<>();
-
- ProvenanceQuery pq=null;
- ProvenanceWriter pw = null;
-
- protected Map<String, ProcessorEnactment> invocationProcessToProcessEnactment = new ConcurrentHashMap<>();
-
- /**
- * adds the input ProvenanceItem event to the tree structure corresponding
- * to the portName found in the item. Repeated invocations of this method
- * incrementally reconstruct the tree structure for each of the workflow
- * outputs
- *
- * @param root
- */
- public void addWorkflowDataItem(ProvenanceItem provenanceItem) {
- WorkflowDataProvenanceItem workflowDataItem = (WorkflowDataProvenanceItem) provenanceItem;
-
- WorkflowDataNode wdn = new WorkflowDataNode();
- wdn.setProcessId(provenanceItem.getProcessId());
- wdn.setPortName(workflowDataItem.getPortName());
- wdn.setInputPort(workflowDataItem.isInputPort());
- wdn.setValue(workflowDataItem.getData().toString());
- int[] index = workflowDataItem.getIndex();
- String iterationToString = iterationToString(index);
- wdn.setIndex(iterationToString);
- wdn.setWorkflowID(workflowDataItem.getWorkflowId());
-
- if (wdn.getValue().contains("list"))
- wdn.setList(true); // HACK
- else
- wdn.setList(false);
-
- // position this wdn into the tree associated to its portName
- List<WorkflowDataNode> aTree = workflowDataTrees.get(wdn.getPortName());
-
- if (aTree == null) { // first item in the tree
- aTree = new ArrayList<WorkflowDataNode>();
- workflowDataTrees.put(wdn.getPortName(), aTree);
- } else
- // update parent pointers
- for (WorkflowDataNode aNode: aTree)
- if (isParent(wdn.getIndex(), aNode.getIndex())) {
- aNode.setParent(wdn);
-
- // set position in collection as the last index in the vector
- aNode.setRelativePosition(getPosition(aNode));
- }
- aTree.add(wdn);
- }
-
- /**
- * writes records to PortBinding or Collection by traversing the trees<br/>
- * expect this to be invoked after workflow completion
- *
- * @param workflowId
- * the external name of the dataflow (not the UUID)
- * @param workflowRunId
- * the runID
- */
- public void processTrees(DataflowRunComplete completeEvent,
- String workflowRunId) {
- String workflowId = completeEvent.getWorkflowId();
- logger.debug("processing output trees");
-
- // i:inputPortName -> t2Ref
- Map<String, String> workflowPortData = new HashMap<>();
-
- for (Map.Entry<String, List<WorkflowDataNode>> entry : workflowDataTrees
- .entrySet()) {
- String portName = entry.getKey();
- List<WorkflowDataNode> tree = entry.getValue();
-
- PortBinding vb = null;
-
- logger.debug("storing tree for var "+portName+" in workflow with ID "+workflowId+" and instance "+workflowRunId);
- for (WorkflowDataNode node:tree) {
- try {
- if (!node.getWorkflowID().equals(workflowId))
- continue;
-
- if (node.getIndex().equals("[]")) {
- // Store top-level workflow inputs/outputs
- if (! node.getProcessId().equals(completeEvent.getProcessId()))
- //logger.warn("Unexpected process ID " + node.getProcessId() + " expected " + completeEvent.getProcessId());
- continue;
- String portKey = (node.isInputPort() ? "/i:" : "/o:") + node.getPortName();
- workflowPortData.put(portKey, node.getValue());
- }
-
- if (node.isList) {
- logger.debug("creating collection entry for "
- + node.value + " with index " + node.index);
-
- if (node.getParent() != null) {
- logger.debug(" and parent " + node.parent.index);
- // write a collection record to DB
- getPw().addCollection(workflowId, node.getValue(),
- node.getParent().getValue(),
- node.getIndex(), portName, workflowRunId);
- } else
- getPw().addCollection(workflowId, node.getValue(),
- null, node.getIndex(), portName,
- workflowRunId);
- } else {
- logger.debug("creating PortBinding for " + node.value
- + " with index " + node.index);
-
- vb = new PortBinding();
-
- vb.setWorkflowId(workflowId);
- vb.setWorkflowRunId(workflowRunId);
-
- vb.setProcessorName(pq.getWorkflow(workflowId)
- .getExternalName());
-
- // vb.setValueType(); // TODO not sure what to set this to
- vb.setPortName(portName);
- vb.setIteration(node.getIndex());
- vb.setValue(node.getValue());
-
- if (node.getParent() != null) {
- logger.debug(" in collection "
- + node.getParent().value + " with index "
- + node.getParent().getIndex());
-
- vb.setCollIDRef(node.getParent().getValue());
- vb.setPositionInColl(node.getRelativePosition());
- } else
- vb.setPositionInColl(1); // default
-
- try {
- getPw().addPortBinding(vb);
- } catch (SQLException e) {
- logger.debug("Problem processing trees for workflow: "
- + workflowId
- + " instance: "
- + workflowRunId
- + " : updating instead of inserting");
- getPw().updatePortBinding(vb);
- }
- }
- } catch (SQLException e) {
- logger.debug(
- "Database problem processing trees for workflow: "
- + workflowId + " instance: "
- + workflowRunId + " : " + workflowId, e);
- }
- }
- }
-
- List<Port> ports = getPq().getPortsForDataflow(workflowId);
- String processId = completeEvent.getProcessId();
-
- DataflowInvocation invocation = new DataflowInvocation();
- invocation.setDataflowInvocationId(UUID.randomUUID().toString());
- invocation.setWorkflowId(workflowId);
- invocation.setWorkflowRunId(workflowRunId);
-
- String parentProcessId = parentProcess(processId, 1);
- if (parentProcessId != null) {
- ProcessorEnactment procAct = invocationProcessToProcessEnactment
- .get(parentProcessId);
- if (procAct != null)
- invocation.setParentProcessorEnactmentId(procAct
- .getProcessEnactmentId());
- }
-
- invocation.setInvocationStarted(workflowStarted.get(completeEvent
- .getParentId()));
- invocation.setInvocationEnded(completeEvent.getInvocationEnded());
- invocation.setCompleted(completeEvent.getState()
- .equals(State.completed));
-
- // Register data
- String inputsDataBindingId = UUID.randomUUID().toString();
- String outputsDataBindingId = UUID.randomUUID().toString();
- for (Port port : ports) {
- String portKey = (port.isInputPort() ? "/i:" : "/o:")
- + port.getPortName();
- String t2Reference = workflowPortData.get(portKey);
- if (t2Reference == null) {
- logger.warn("No workflow port data for " + portKey);
- continue;
- }
- DataBinding dataBinding = new DataBinding();
- dataBinding
- .setDataBindingId(port.isInputPort() ? inputsDataBindingId
- : outputsDataBindingId);
- dataBinding.setPort(port);
- dataBinding.setT2Reference(t2Reference);
- dataBinding.setWorkflowRunId(workflowRunId);
- try {
- pw.addDataBinding(dataBinding);
- } catch (SQLException e) {
- logger.warn("Could not add databinding for " + portKey, e);
- }
- }
-
- invocation.setInputsDataBindingId(inputsDataBindingId);
- invocation.setOutputsDataBindingId(outputsDataBindingId);
- try {
- pw.addDataflowInvocation(invocation);
- } catch (SQLException e) {
- logger.warn("Could not store dataflow invocation for " + processId,
- e);
- }
- }
-
-
- /**
- * @param node
- * @return the last digit in the index
- */
- private int getPosition(WorkflowDataNode node) {
- String[] vector = node.getIndex()
- .substring(1, node.getIndex().length() - 1).split(",");
- //TODO need some logic here to avoid trying to parse "" as integer, this is my try
-
- if ((vector[vector.length-1]).equals(""))
- return 1;
- return Integer.parseInt(vector[vector.length - 1]) + 1;
- }
-
- private boolean isParent(String index1, String index2) {
- // strip first and last '[' ']'
- String index11 = index1.substring(1, index1.length() - 1);
- String index22 = index2.substring(1, index2.length() - 1);
-
- String[] tokens1 = index11.split(",");
- String[] tokens2 = index22.split(",");
-
- // [] cannot be parent of [x1,x2,...] with >= 2 elements
- if (index11.equals("") && tokens2.length > 1)
- return false;
-
- // [] is parent of any [x]
- if (index11.equals("") && tokens2.length == 1)
- return true;
-
- // [x1,x2, ...,xk] cannot be parent of [x1,x2,...xh] when k < h-1
- // because [x1,x2,...xh] is more than one level deeper than [x1,x2, ...,xk]
- if (tokens1.length != tokens2.length - 1)
- return false;
-
- return index22.startsWith(index11);
- }
-
- static class WorkflowDataNode {
- private String portName;
- private String value;
- private String index;
- private String workflowID;
- private int relativePosition;
- private boolean isList;
- private WorkflowDataNode parent;
- private String processId;
- private boolean isInputPort;
-
- public String getProcessId() {
- return processId;
- }
-
- /**
- * @return the value
- */
- public String getValue() {
- return value;
- }
-
- public void setProcessId(String processId) {
- this.processId = processId;
-
- }
-
- /**
- * @param value
- * the value to set
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * @return the index
- */
- public String getIndex() {
- return index;
- }
-
- /**
- * @param index
- * the index to set
- */
- public void setIndex(String index) {
- this.index = index;
- }
-
- /**
- * @return the portName
- */
- public String getPortName() {
- return portName;
- }
-
- /**
- * @param portName
- * the portName to set
- */
- public void setPortName(String portName) {
- this.portName = portName;
- }
-
- /**
- * @return the isList
- */
- public boolean isList() {
- return isList;
- }
-
- /**
- * @param isList
- * the isList to set
- */
- public void setList(boolean isList) {
- this.isList = isList;
- }
-
- /**
- * @return the parent
- */
- public WorkflowDataNode getParent() {
- return parent;
- }
-
- /**
- * @param parent
- * the parent to set
- */
- public void setParent(WorkflowDataNode parent) {
- this.parent = parent;
- }
-
- /**
- * @return the relativePosition
- */
- public int getRelativePosition() {
- return relativePosition;
- }
-
- /**
- * @param relativePosition
- * the relativePosition to set
- */
- public void setRelativePosition(int relativePosition) {
- this.relativePosition = relativePosition;
- }
-
- /**
- * @return the workflowID
- */
- public String getWorkflowID() {
- return workflowID;
- }
-
- /**
- * @param workflowID
- * the workflowID to set
- */
- public void setWorkflowID(String workflowID) {
- this.workflowID = workflowID;
- }
-
- public void setInputPort(boolean isInputPort) {
- this.isInputPort = isInputPort;
- }
-
- public boolean isInputPort() {
- return isInputPort;
- }
- }
-
- /**
- * @return the pq
- */
- public ProvenanceQuery getPq() {
- return pq;
- }
-
- /**
- * @param pq
- * the pq to set
- */
- public void setPq(ProvenanceQuery pq) {
- this.pq = pq;
- }
-
- /**
- * @return the pw
- */
- public ProvenanceWriter getPw() {
- return pw;
- }
-
- /**
- * @param pw
- * the pw to set
- */
- public void setPw(ProvenanceWriter pw) {
- this.pw = pw;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ActivityType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ActivityType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ActivityType.java
deleted file mode 100644
index b5f8644..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ActivityType.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-import net.sf.taverna.t2.provenance.lineageservice.types.ProvenanceEventType;
-
-/**
- *
- * @author Paolo Missier
- *
- */
-public class ActivityType implements ProvenanceEventType {
- private IterationType[] iteration;
-
- private String id; // attribute
-
- public ActivityType() {
- }
-
- public ActivityType(IterationType[] iteration, String id) {
- this.iteration = iteration;
- this.id = id;
- }
-
- /**
- * Gets the iteration value for this ActivityType.
- *
- * @return iteration
- */
- public IterationType[] getIteration() {
- return iteration;
- }
-
- /**
- * Sets the iteration value for this ActivityType.
- *
- * @param iteration
- */
- public void setIteration(IterationType[] iteration) {
- this.iteration = iteration;
- }
-
- public IterationType getIteration(int i) {
- return this.iteration[i];
- }
-
- public void setIteration(int i, IterationType _value) {
- this.iteration[i] = _value;
- }
-
- /**
- * Gets the id value for this ActivityType.
- *
- * @return id
- */
- public java.lang.String getId() {
- return id;
- }
-
- /**
- * Sets the id value for this ActivityType.
- *
- * @param id
- */
- public void setId(java.lang.String id) {
- this.id = id;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/DataDocumentType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/DataDocumentType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/DataDocumentType.java
deleted file mode 100644
index 27fa322..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/DataDocumentType.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-/**
- *
- * @author Paolo Missier
- *
- */
-public class DataDocumentType implements ProvenanceEventType {
- private String reference;
- private String id; // attribute
-
- public DataDocumentType() {
- }
-
- public DataDocumentType(String reference, String id) {
- this.reference = reference;
- this.id = id;
- }
-
- /**
- * Gets the reference value for this DataDocumentType.
- *
- * @return reference
- */
- public String getReference() {
- return reference;
- }
-
- /**
- * Sets the reference value for this DataDocumentType.
- *
- * @param reference
- */
- public void setReference(String reference) {
- this.reference = reference;
- }
-
- /**
- * Gets the id value for this DataDocumentType.
- *
- * @return id
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the id value for this DataDocumentType.
- *
- * @param id
- */
- public void setId(String id) {
- this.id = id;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/IterationType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/IterationType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/IterationType.java
deleted file mode 100644
index be5389b..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/IterationType.java
+++ /dev/null
@@ -1,96 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-/**
- *
- * @author Paolo Missier
- *
- */
-public class IterationType implements ProvenanceEventType {
- private PortsSequenceType inputdata;
- private PortsSequenceType outputdata;
- private String id; // attribute
-
- public IterationType() {
- }
-
- public IterationType(PortsSequenceType inputdata,
- PortsSequenceType outputdata, String id) {
- this.inputdata = inputdata;
- this.outputdata = outputdata;
- this.id = id;
- }
-
- /**
- * Gets the inputdata value for this IterationType.
- *
- * @return inputdata
- */
- public PortsSequenceType getInputdata() {
- return inputdata;
- }
-
- /**
- * Sets the inputdata value for this IterationType.
- *
- * @param inputdata
- */
- public void setInputdata(PortsSequenceType inputdata) {
- this.inputdata = inputdata;
- }
-
- /**
- * Gets the outputdata value for this IterationType.
- *
- * @return outputdata
- */
- public PortsSequenceType getOutputdata() {
- return outputdata;
- }
-
- /**
- * Sets the outputdata value for this IterationType.
- *
- * @param outputdata
- */
- public void setOutputdata(PortsSequenceType outputdata) {
- this.outputdata = outputdata;
- }
-
- /**
- * Gets the id value for this IterationType.
- *
- * @return id
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the id value for this IterationType.
- *
- * @param id
- */
- public void setId(String id) {
- this.id = id;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/LiteralType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/LiteralType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/LiteralType.java
deleted file mode 100644
index 2b87758..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/LiteralType.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-/**
- *
- * @author Paolo Missier
- *
- */
-public class LiteralType implements ProvenanceEventType {
- private String id; // attribute
-
- public LiteralType() {
- }
-
- public LiteralType(String id) {
- this.id = id;
- }
-
- /**
- * Gets the id value for this LiteralType.
- *
- * @return id
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the id value for this LiteralType.
- *
- * @param id
- */
- public void setId(String id) {
- this.id = id;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/PortType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/PortType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/PortType.java
deleted file mode 100644
index 6978ac9..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/PortType.java
+++ /dev/null
@@ -1,96 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-/**
- *
- * @author Paolo Missier
- *
- */
-public class PortType implements ProvenanceEventType {
- private DataDocumentType dataDocument;
- private LiteralType literal;
- private String name; // attribute
-
- public PortType() {
- }
-
- public PortType(DataDocumentType dataDocument, LiteralType literal,
- String name) {
- this.dataDocument = dataDocument;
- this.literal = literal;
- this.name = name;
- }
-
- /**
- * Gets the dataDocument value for this PortType.
- *
- * @return dataDocument
- */
- public DataDocumentType getDataDocument() {
- return dataDocument;
- }
-
- /**
- * Sets the dataDocument value for this PortType.
- *
- * @param dataDocument
- */
- public void setDataDocument(DataDocumentType dataDocument) {
- this.dataDocument = dataDocument;
- }
-
- /**
- * Gets the literal value for this PortType.
- *
- * @return literal
- */
- public LiteralType getLiteral() {
- return literal;
- }
-
- /**
- * Sets the literal value for this PortType.
- *
- * @param literal
- */
- public void setLiteral(LiteralType literal) {
- this.literal = literal;
- }
-
- /**
- * Gets the name value for this PortType.
- *
- * @return name
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the name value for this PortType.
- *
- * @param name
- */
- public void setName(String name) {
- this.name = name;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/PortsSequenceType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/PortsSequenceType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/PortsSequenceType.java
deleted file mode 100644
index 5eddde8..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/PortsSequenceType.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-/**
- *
- * @author Paolo Missier
- *
- */
-public class PortsSequenceType implements ProvenanceEventType {
- private PortType[] port;
-
- public PortsSequenceType() {
- }
-
- public PortsSequenceType(PortType[] port) {
- this.port = port;
- }
-
- /**
- * Gets the port value for this PortsSequenceType.
- *
- * @return port
- */
- public PortType[] getPort() {
- return port;
- }
-
- /**
- * Sets the port value for this PortsSequenceType.
- *
- * @param port
- */
- public void setPort(PortType[] port) {
- this.port = port;
- }
-
- public PortType getPort(int i) {
- return this.port[i];
- }
-
- public void setPort(int i, PortType _value) {
- this.port[i] = _value;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProcessType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProcessType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProcessType.java
deleted file mode 100644
index 163bc93..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProcessType.java
+++ /dev/null
@@ -1,105 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-/**
- *
- * @author Paolo Missier
- *
- */
-public class ProcessType implements ProvenanceEventType {
- private ProcessorType[] processor;
- private String dataflowID; // attribute
- private String facadeID; // attribute
-
- public ProcessType() {
- }
-
- public ProcessType(ProcessorType[] processor, String dataflowID,
- String facadeID) {
- this.processor = processor;
- this.dataflowID = dataflowID;
- this.facadeID = facadeID;
- }
-
- /**
- * Gets the processor value for this ProcessType.
- *
- * @return processor
- */
- public ProcessorType[] getProcessor() {
- return processor;
- }
-
- /**
- * Sets the processor value for this ProcessType.
- *
- * @param processor
- */
- public void setProcessor(ProcessorType[] processor) {
- this.processor = processor;
- }
-
- public ProcessorType getProcessor(int i) {
- return this.processor[i];
- }
-
- public void setProcessor(int i, ProcessorType _value) {
- this.processor[i] = _value;
- }
-
- /**
- * Gets the dataflowID value for this ProcessType.
- *
- * @return dataflowID
- */
- public String getDataflowID() {
- return dataflowID;
- }
-
- /**
- * Sets the dataflowID value for this ProcessType.
- *
- * @param dataflowID
- */
- public void setDataflowID(String dataflowID) {
- this.dataflowID = dataflowID;
- }
-
- /**
- * Gets the facadeID value for this ProcessType.
- *
- * @return facadeID
- */
- public String getFacadeID() {
- return facadeID;
- }
-
- /**
- * Sets the facadeID value for this ProcessType.
- *
- * @param facadeID
- */
- public void setFacadeID(String facadeID) {
- this.facadeID = facadeID;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProcessorType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProcessorType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProcessorType.java
deleted file mode 100644
index 53285df..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProcessorType.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-/**
- *
- * @author Paolo Missier
- *
- */
-public class ProcessorType implements ProvenanceEventType {
- private ActivityType[] activity;
- private String id; // attribute
-
- public ProcessorType() {
- }
-
- public ProcessorType(ActivityType[] activity, String id) {
- this.activity = activity;
- this.id = id;
- }
-
- /**
- * Gets the activity value for this ProcessorType.
- *
- * @return activity
- */
- public ActivityType[] getActivity() {
- return activity;
- }
-
- /**
- * Sets the activity value for this ProcessorType.
- *
- * @param activity
- */
- public void setActivity(ActivityType[] activity) {
- this.activity = activity;
- }
-
- public ActivityType getActivity(int i) {
- return this.activity[i];
- }
-
- public void setActivity(int i, ActivityType _value) {
- this.activity[i] = _value;
- }
-
- /**
- * Gets the id value for this ProcessorType.
- *
- * @return id
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the id value for this ProcessorType.
- *
- * @param id
- */
- public void setId(String id) {
- this.id = id;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProvenanceEventType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProvenanceEventType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProvenanceEventType.java
deleted file mode 100644
index 6ebe680..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/types/ProvenanceEventType.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.types;
-
-/**
- * Used by an implementation of Provenance to identify the item type
- *
- * @author Paolo Missier
- */
-public interface ProvenanceEventType {
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Activity.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Activity.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Activity.java
deleted file mode 100644
index 819fce8..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Activity.java
+++ /dev/null
@@ -1,63 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-public class Activity {
- private String activityId;
-
- @Override
- public int hashCode() {
- return 31 + ((activityId == null) ? 0 : activityId.hashCode());
- }
-
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("Activity [activityDefinition=");
- builder.append(activityDefinition);
- builder.append("]");
- return builder.toString();
- }
-
- @Override
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- Activity other = (Activity) obj;
- if (activityId == null) {
- if (other.activityId != null)
- return false;
- } else if (!activityId.equals(other.activityId))
- return false;
- return true;
- }
-
- private String activityDefinition;
- private Workflow workflow;
-
- public String getActivityId() {
- return activityId;
- }
-
- public void setActivityId(String activityId) {
- this.activityId = activityId;
- }
-
- public String getActivityDefinition() {
- return activityDefinition;
- }
-
- public void setActivityDefinition(String activityDefinition) {
- this.activityDefinition = activityDefinition;
- }
-
- public Workflow getWorkflow() {
- return workflow;
- }
-
- public void setWorkflow(Workflow workflow) {
- this.workflow = workflow;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Collection.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Collection.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Collection.java
deleted file mode 100644
index 56340db..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Collection.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-public class Collection {
- private String identifier;
- private String parentIdentifier;
- private String workflowRunIdentifier;
- private String processorName;
- private String portName;
- private String iteration;
- private String collId;
-
- public String getIdentifier() {
- return identifier;
- }
-
- public void setIdentifier(String identifier) {
- this.identifier = identifier;
- }
-
- public String getParentIdentifier() {
- return parentIdentifier;
- }
-
- public void setParentIdentifier(String parentIdentifier) {
- this.parentIdentifier = parentIdentifier;
- }
-
- public String getWorkflowRunIdentifier() {
- return workflowRunIdentifier;
- }
-
- public void setWorkflowRunIdentifier(String workflowRunIdentifier) {
- this.workflowRunIdentifier = workflowRunIdentifier;
- }
-
- public String getProcessorName() {
- return processorName;
- }
-
- public void setProcessorName(String processorName) {
- this.processorName = processorName;
- }
-
- public String getPortName() {
- return portName;
- }
-
- public void setPortName(String portName) {
- this.portName = portName;
- }
-
- public String getIteration() {
- return iteration;
- }
-
- public void setIteration(String iteration) {
- this.iteration = iteration;
- }
-
- public void setCollId(String collId) {
- this.collId = collId;
- }
-
- public String getCollId() {
- return collId;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DDRecord.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DDRecord.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DDRecord.java
deleted file mode 100644
index ec762c0..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DDRecord.java
+++ /dev/null
@@ -1,149 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-/**
- * a simple bean to hold a database record from the DD table
- *
- * @author paolo
- *
- */
-public class DDRecord {
-
- private String PFrom;
- private String PTo;
- private String vTo;
- private String valTo;
- private String vFrom;
- private String valFrom;
- private String iteration;
- public boolean isInput;
-
- @Override
- public String toString() {
- return new String("proc: " + PFrom + " vFrom: " + vFrom + " valFrom: "
- + valFrom + "PTo: " + PTo + " vTo: " + vTo + " valTo: " + valTo);
- }
-
- /**
- * @return the vTo
- */
- public String getVTo() {
- return vTo;
- }
-
- /**
- * @param to
- * the vTo to set
- */
- public void setVTo(String to) {
- vTo = to;
- }
-
- /**
- * @return the valTo
- */
- public String getValTo() {
- return valTo;
- }
-
- /**
- * @param valTo
- * the valTo to set
- */
- public void setValTo(String valTo) {
- this.valTo = valTo;
- }
-
- /**
- * @return the vFrom
- */
- public String getVFrom() {
- return vFrom;
- }
-
- /**
- * @param from
- * the vFrom to set
- */
- public void setVFrom(String from) {
- vFrom = from;
- }
-
- /**
- * @return the valFrom
- */
- public String getValFrom() {
- return valFrom;
- }
-
- /**
- * @param valFrom
- * the valFrom to set
- */
- public void setValFrom(String valFrom) {
- this.valFrom = valFrom;
- }
-
- /**
- * @return the isInput
- */
- public boolean isInput() {
- return isInput;
- }
-
- /**
- * @param isInput
- * the isInput to set
- */
- public void setInput(boolean isInput) {
- this.isInput = isInput;
- }
-
- /**
- * @return the pFrom
- */
- public String getPFrom() {
- return PFrom;
- }
-
- /**
- * @param from
- * the pFrom to set
- */
- public void setPFrom(String from) {
- PFrom = from;
- }
-
- /**
- * @return the pTo
- */
- public String getPTo() {
- return PTo;
- }
-
- /**
- * @param to
- * the pTo to set
- */
- public void setPTo(String to) {
- PTo = to;
- }
-
- /**
- * @return the iteration
- */
- public String getIteration() {
- return iteration;
- }
-
- /**
- * @param iteration
- * the iteration to set
- */
- public void setIteration(String iteration) {
- this.iteration = iteration;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataBinding.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataBinding.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataBinding.java
deleted file mode 100644
index 3b4f123..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataBinding.java
+++ /dev/null
@@ -1,82 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-public class DataBinding {
- private String dataBindingId;
- private Port port;
- private String t2Reference;
- private String workflowRunId;
-
- public String getDataBindingId() {
- return dataBindingId;
- }
-
- public void setDataBindingId(String dataBindingId) {
- this.dataBindingId = dataBindingId;
- }
-
- public Port getPort() {
- return port;
- }
-
- public void setPort(Port port) {
- this.port = port;
- }
-
- @Override
- public int hashCode() {
- int result = 31 + ((dataBindingId == null) ? 0 : dataBindingId
- .hashCode());
- return 31 * result + ((port == null) ? 0 : port.hashCode());
- }
-
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("DataBinding [dataBindingId=");
- builder.append(dataBindingId);
- builder.append(", port=");
- builder.append(port);
- builder.append(", t2Reference=");
- builder.append(t2Reference);
- builder.append("]");
- return builder.toString();
- }
-
- @Override
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- DataBinding other = (DataBinding) obj;
- if (dataBindingId == null) {
- if (other.dataBindingId != null)
- return false;
- } else if (!dataBindingId.equals(other.dataBindingId))
- return false;
- if (port == null) {
- if (other.port != null)
- return false;
- } else if (!port.equals(other.port))
- return false;
- return true;
- }
-
- public String getT2Reference() {
- return t2Reference;
- }
-
- public void setT2Reference(String t2Reference) {
- this.t2Reference = t2Reference;
- }
-
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataLink.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataLink.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataLink.java
deleted file mode 100644
index db2e42a..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataLink.java
+++ /dev/null
@@ -1,127 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-/**
- * @author paolo
- *
- */
-
-public class DataLink {
- private String workflowId;
- private String sourcePortId;
- private String sourceProcessorName;
- private String sourcePortName;
- private String destinationPortId;
- private String destinationProcessorName;
- private String destinationPortName;
-
- /**
- * @return the workflowId
- */
- public String getWorkflowId() {
- return workflowId;
- }
-
- /**
- * @param workflowId
- * the workflowId to set
- */
- public void setWorkflowId(String workflowRunId) {
- this.workflowId = workflowRunId;
- }
-
- public String getSourcePortId() {
- return sourcePortId;
- }
-
- public void setSourcePortId(String sourcePortId) {
- this.sourcePortId = sourcePortId;
- }
-
- /**
- * @return the sourceProcessorName
- */
- public String getSourceProcessorName() {
- return sourceProcessorName;
- }
-
- /**
- * @param sourceProcessorName
- * the sourceProcessorName to set
- */
- public void setSourceProcessorName(String sourceProcessorName) {
- this.sourceProcessorName = sourceProcessorName;
- }
-
- /**
- * @return the sourcePortName
- */
- public String getSourcePortName() {
- return sourcePortName;
- }
-
- /**
- * @param sourcePortName
- * the sourcePortName to set
- */
- public void setSourcePortName(String sourcePortName) {
- this.sourcePortName = sourcePortName;
- }
-
- public String getDestinationPortId() {
- return destinationPortId;
- }
-
- public void setDestinationPortId(String destinationPortId) {
- this.destinationPortId = destinationPortId;
- }
-
- /**
- * @return the sourceprocessorNameRef
- */
- public String getDestinationProcessorName() {
- return destinationProcessorName;
- }
-
- /**
- * @param sourceprocessorNameRef
- * the sourceprocessorNameRef to set
- */
- public void setDestinationProcessorName(String destinationProcessorName) {
- this.destinationProcessorName = destinationProcessorName;
- }
-
- /**
- * @return the destinationPortName
- */
- public String getDestinationPortName() {
- return destinationPortName;
- }
-
- /**
- * @param destinationPortName
- * the destinationPortName to set
- */
- public void setDestinationPortName(String destinationPortName) {
- this.destinationPortName = destinationPortName;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataValueExtractor.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataValueExtractor.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataValueExtractor.java
deleted file mode 100644
index 8480197..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataValueExtractor.java
+++ /dev/null
@@ -1,23 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-/**
- * @author paolo
- *
- */
-public interface DataValueExtractor {
-
- /**
- * extracts a printable string from a more complex object. This is not the
- * same as toString() as it is applied to an object, rather than being a
- * method on the object itself
- *
- * @param complexContent
- * should really be a byte array FIXME
- * @return
- */
- public String extractString(Object complexContent);
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataflowInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataflowInvocation.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataflowInvocation.java
deleted file mode 100644
index f838f79..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/DataflowInvocation.java
+++ /dev/null
@@ -1,118 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-import java.sql.Timestamp;
-
-public class DataflowInvocation {
- private String dataflowInvocationId;
- private String workflowId;
- private String workflowRunId;
- private String parentProcessorEnactmentId;
- private String inputsDataBindingId;
- private String outputsDataBindingId;
- private Timestamp invocationEnded;
- private Timestamp invocationStarted;
- private boolean completed;
-
- @Override
- public int hashCode() {
- return 31 + ((dataflowInvocationId == null) ? 0 : dataflowInvocationId
- .hashCode());
- }
-
- @Override
- public String toString() {
- return "DataflowInvocation [dataflowInvocationId="
- + dataflowInvocationId + ", parentProcessorEnactmentId="
- + parentProcessorEnactmentId + ", workflowRunId="
- + workflowRunId + "]";
- }
-
- @Override
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- DataflowInvocation other = (DataflowInvocation) obj;
- if (dataflowInvocationId == null) {
- if (other.dataflowInvocationId != null)
- return false;
- } else if (!dataflowInvocationId.equals(other.dataflowInvocationId))
- return false;
- return true;
- }
-
- public String getDataflowInvocationId() {
- return dataflowInvocationId;
- }
-
- public void setDataflowInvocationId(String dataflowInvocationId) {
- this.dataflowInvocationId = dataflowInvocationId;
- }
-
- public String getWorkflowId() {
- return workflowId;
- }
-
- public void setWorkflowId(String workflowId) {
- this.workflowId = workflowId;
- }
-
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-
- public String getParentProcessorEnactmentId() {
- return parentProcessorEnactmentId;
- }
-
- public void setParentProcessorEnactmentId(String parentProcessorEnactmentId) {
- this.parentProcessorEnactmentId = parentProcessorEnactmentId;
- }
-
- public String getInputsDataBindingId() {
- return inputsDataBindingId;
- }
-
- public void setInputsDataBindingId(String inputsDataBindingId) {
- this.inputsDataBindingId = inputsDataBindingId;
- }
-
- public String getOutputsDataBindingId() {
- return outputsDataBindingId;
- }
-
- public void setOutputsDataBindingId(String outputsDataBindingId) {
- this.outputsDataBindingId = outputsDataBindingId;
- }
-
- public Timestamp getInvocationEnded() {
- return invocationEnded;
- }
-
- public void setInvocationEnded(Timestamp invocationEnded) {
- this.invocationEnded = invocationEnded;
- }
-
- public Timestamp getInvocationStarted() {
- return invocationStarted;
- }
-
- public void setInvocationStarted(Timestamp invocationStarted) {
- this.invocationStarted = invocationStarted;
- }
-
- public void setCompleted(boolean completed) {
- this.completed = completed;
- }
-
- public boolean getCompleted() {
- return completed;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/NestedListNode.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/NestedListNode.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/NestedListNode.java
deleted file mode 100644
index c17a11d..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/NestedListNode.java
+++ /dev/null
@@ -1,107 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-/**
- * @author paolo
- *
- */
-public class NestedListNode {
- private String collectionT2Reference;
- private String parentCollectionT2Reference;
- private String workflowRunId;
- private String processorName;
- private String portName;
- private String iteration;
-
- /**
- * @return the collectionT2Reference
- */
- public String getCollectionT2Reference() {
- return collectionT2Reference;
- }
-
- /**
- * @param collectionT2Reference
- * the collectionT2Reference to set
- */
- public void setCollectionT2Reference(String collectionT2Reference) {
- this.collectionT2Reference = collectionT2Reference;
- }
-
- /**
- * @return the parentCollIdRef
- */
- public String getParentCollIdRef() {
- return parentCollectionT2Reference;
- }
-
- /**
- * @param parentCollIdRef
- * the parentCollIdRef to set
- */
- public void setParentCollIdRef(String parentCollIdRef) {
- this.parentCollectionT2Reference = parentCollIdRef;
- }
-
- /**
- * @return the workflowRunId
- */
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- /**
- * @param workflowRunId
- * the workflowRunId to set
- */
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-
- /**
- * @return the processorNameRef
- */
- public String getProcessorName() {
- return processorName;
- }
-
- /**
- * @param nameRef
- * the processorNameRef to set
- */
- public void setProcessorName(String nameRef) {
- processorName = nameRef;
- }
-
- /**
- * @return the portName
- */
- public String getPortName() {
- return portName;
- }
-
- /**
- * @param portName
- * the portName to set
- */
- public void setPortName(String portName) {
- this.portName = portName;
- }
-
- /**
- * @return the iteration
- */
- public String getIteration() {
- return iteration;
- }
-
- /**
- * @param iteration
- * the iteration to set
- */
- public void setIteration(String iteration) {
- this.iteration = iteration;
- }
-}