http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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/3ecb1291/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; - } -}
