[09/12] incubator-taverna-engine git commit: some provenance refactoring

[re...@apache.org]

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/ProvenanceQuery.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/ProvenanceQuery.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/ProvenanceQuery.java
deleted file mode 100644
index 4b318fc..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/ProvenanceQuery.java
+++ /dev/null
@@ -1,2069 +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 static net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector.DataflowInvocationTable.parentProcessorEnactmentId;
-import static net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceProcessor.DATAFLOW_ACTIVITY;
-
-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.sql.Timestamp;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.ListIterator;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector.CollectionTable;
-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.lineageservice.utils.Collection;
-import net.sf.taverna.t2.provenance.lineageservice.utils.DDRecord;
-import net.sf.taverna.t2.provenance.lineageservice.utils.DataLink;
-import net.sf.taverna.t2.provenance.lineageservice.utils.DataflowInvocation;
-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.ProcessorEnactment;
-import net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceProcessor;
-import net.sf.taverna.t2.provenance.lineageservice.utils.Workflow;
-import net.sf.taverna.t2.provenance.lineageservice.utils.WorkflowTree;
-import net.sf.taverna.t2.provenance.lineageservice.utils.WorkflowRun;
-
-import org.apache.log4j.Logger;
-import org.jdom.Document;
-import org.jdom.Element;
-
-import uk.org.taverna.configuration.database.DatabaseManager;
-
-/**
- * Handles all the querying of provenance items in the database layer. Uses
- * standard SQL so all specific instances of this class can extend this writer
- * to handle all of the db queries
- *
- * @author Paolo Missier
- * @author Ian Dunlop
- * @author Stuart Owen
- *
- */
-public abstract class ProvenanceQuery {
-	protected Logger logger = Logger.getLogger(ProvenanceQuery.class);
-	private final DatabaseManager databaseManager;
-
-	public ProvenanceQuery(DatabaseManager databaseManager) {
-		this.databaseManager = databaseManager;
-	}
-
-	public Connection getConnection() throws InstantiationException,
-			IllegalAccessException, ClassNotFoundException, SQLException {
-		return databaseManager.getConnection();
-	}
-
-	private Q query(String baseQuery) {
-		return new Q(baseQuery);
-	}
-	private class Q {
-		private String q;
-		private Map<String,String>where;
-		private List<String> order;
-
-		Q(String baseQuery) {
-			q = baseQuery;
-		}
-
-		public Q where(String key, String value) {
-			if (where == null)
-				where = new HashMap<>();
-			where.put(key, value);
-			return this;
-		}
-
-		public Q where(Map<String, String> clauses) {
-			if (where == null)
-				where = new HashMap<>();
-			where.putAll(clauses);
-			return this;
-		}
-
-		public Q orderBy(String key) {
-			if (order == null)
-				order = new ArrayList<>();
-			order.add(key);
-			return this;
-		}
-		public ResultSet exec(Statement statement) throws SQLException {
-			return statement.executeQuery(query());
-		}
-		public String query() {
-			return addOrderByToQuery(addWhereClauseToQuery(q, where, false), order, false);
-		}
-	}
-
-	/**
-	 * implements a set of query constraints of the form var = value into a
-	 * WHERE clause
-	 *
-	 * @param q
-	 * @param queryConstraints
-	 * @return
-	 */
-	protected String addWhereClauseToQuery(String q,
-			Map<String, String> queryConstraints, boolean terminate) {
-
-		// complete query according to constraints
-		StringBuilder buffer = new StringBuilder(q);
-
-		String sep = " WHERE ";
-		if (queryConstraints != null)
-			for (Entry<String, String> entry : queryConstraints.entrySet()) {
-				buffer.append(sep).append(entry.getKey())
-						.append(" = \'").append(entry.getValue()).append("\' ");
-				sep = " AND ";
-			}
-		return buffer.toString();
-	}
-
-	protected String addOrderByToQuery(String q, List<String> orderAttr,
-			boolean terminate) {
-		// complete query according to constraints
-		StringBuilder buffer = new StringBuilder(q);
-
-		String sep = " ORDER BY ";
-		if (orderAttr != null)
-			for (String attr : orderAttr) {
-				buffer.append(sep).append(attr);
-				sep = ",";
-			}
-		return buffer.toString();
-	}
-
-	/**
-	 * select Port records that satisfy constraints
-	 */
-	public List<Port> getPorts(Map<String, String> queryConstraints)
-			throws SQLException {
-		List<Port> result = new ArrayList<>();
-
-		try (Connection connection = getConnection();
-				Statement stmt = connection.createStatement();
-				ResultSet rs = query(
-						"SELECT DISTINCT V.* FROM Port V "
-								+ "JOIN WorkflowRun W ON W.workflowId = V.workflowId")
-						.where(queryConstraints)
-						.orderBy("V.iterationStrategyOrder").exec(stmt)) {
-			while (rs.next()) {
-				Port aPort = new Port();
-
-				aPort.setWorkflowId(rs.getString("workflowId"));
-				aPort.setInputPort(rs.getBoolean("isInputPort"));
-				aPort.setIdentifier(rs.getString("portId"));
-				aPort.setProcessorName(rs.getString("processorName"));
-				aPort.setProcessorId(rs.getString("processorId"));
-				aPort.setPortName(rs.getString("portName"));
-				aPort.setDepth(rs.getInt("depth"));
-				if (rs.getString("resolvedDepth") != null)
-					aPort.setResolvedDepth(rs.getInt("resolvedDepth"));
-				result.add(aPort);
-			}
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-
-
-	/**
-	 * return the input variables for a given processor and a workflowRunId
-	 *
-	 * @param pname
-	 * @param workflowRunId
-	 * @return list of input variables
-	 * @throws SQLException
-	 */
-	public List<Port> getInputPorts(String pname, String wfID)
-			throws SQLException {
-		// get (var, proc) from Port to see if it's input/output
-		Map<String, String> varQueryConstraints = new HashMap<>();
-
-		varQueryConstraints.put("V.workflowId", wfID);
-		varQueryConstraints.put("V.processorName", pname);
-		varQueryConstraints.put("V.isInputPort", "1");
-		return getPorts(varQueryConstraints);
-	}
-
-	/**
-	 * return the output variables for a given processor and a workflowRunId
-	 *
-	 * @param pname
-	 * @param workflowRunId
-	 * @return list of output variables
-	 * @throws SQLException
-	 */
-	public List<Port> getOutputPorts(String pname, String wfID)
-			throws SQLException {
-		// get (var, proc) from Port to see if it's input/output
-		Map<String, String> varQueryConstraints = new HashMap<>();
-
-		varQueryConstraints.put("V.workflowId", wfID);
-		varQueryConstraints.put("V.processorName", pname);
-		varQueryConstraints.put("V.isInputPort", "0");
-		return getPorts(varQueryConstraints);
-	}
-
-	/**
-	 * selects all Datalinks
-	 *
-	 * @param queryConstraints
-	 * @return
-	 * @throws SQLException
-	 */
-	public List<DataLink> getDataLinks(Map<String, String> queryConstraints)
-			throws SQLException {
-		List<DataLink> result = new ArrayList<>();
-
-		String q = addWhereClauseToQuery("SELECT A.* FROM Datalink A", queryConstraints, true);
-
-		try (Connection connection = getConnection();
-				Statement stmt = connection.createStatement()) {
-			ResultSet rs = stmt.executeQuery(q);
-			while (rs.next()) {
-				DataLink aDataLink = new DataLink();
-
-				aDataLink.setWorkflowId(rs.getString("workflowId"));
-				aDataLink.setSourceProcessorName(rs
-						.getString("sourceProcessorName"));
-				aDataLink.setSourcePortName(rs.getString("sourcePortName"));
-				aDataLink.setDestinationProcessorName(rs
-						.getString("destinationProcessorName"));
-				aDataLink.setDestinationPortName(rs
-						.getString("destinationPortName"));
-				aDataLink.setSourcePortId(rs.getString("sourcePortId"));
-				aDataLink.setDestinationPortId(rs
-						.getString("destinationPortId"));
-				result.add(aDataLink);
-			}
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-
-		return result;
-	}
-
-	public String getTopLevelWorkflowIdForRun(String runID) throws SQLException {
-		for (Workflow w : getWorkflowsForRun(runID))
-			if (w.getParentWorkflowId() == null)
-				return w.getWorkflowId();
-		return null;
-	}
-
-	/**
-	 * returns the names of all workflows (top level + nested) for a given runID
-	 * @param runID
-	 * @return
-	 * @throws SQLException
-	 */
-	public List<String> getWorkflowIdsForRun(String runID) throws SQLException {
-		List<String> workflowIds = new ArrayList<>();
-		for (Workflow w : getWorkflowsForRun(runID))
-			workflowIds.add(w.getWorkflowId());
-		return workflowIds;
-	}
-
-	/**
-	 * returns the workflows associated to a single runID
-	 * @param runID
-	 * @return
-	 * @throws SQLException
-	 */
-	public List<Workflow> getWorkflowsForRun(String runID) throws SQLException {
-		List<Workflow> result = new ArrayList<>();
-		String q = "SELECT DISTINCT W.* FROM WorkflowRun I JOIN Workflow W ON I.workflowId = W.workflowId WHERE workflowRunId = ?";
-		try (Connection connection = getConnection();
-				PreparedStatement stmt = connection.prepareStatement(q)) {
-			stmt.setString(1, runID);
-			ResultSet rs = stmt.executeQuery();
-			while (rs.next()) {
-				Workflow w = new Workflow();
-				w.setWorkflowId(rs.getString("workflowId"));
-				w.setParentWorkflowId(rs.getString("parentWorkflowId"));
-				result.add(w);
-			}
-		} catch (InstantiationException | IllegalAccessException
-				| ClassNotFoundException e) {
-			logger.error("Error finding the workflow reference", e);
-		}
-		return result;
-	}
-
-	public String getLatestRunID() throws SQLException {
-		String q = "SELECT workflowRunId FROM WorkflowRun ORDER BY timestamp DESC";
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(q)) {
-			ResultSet rs = ps.executeQuery();
-			if (rs.next())
-				return rs.getString("workflowRunId");
-		} catch (Exception e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	/**
-	 * @param dataflowID
-	 * @param conditions currently only understands "from" and "to" as timestamps for range queries
-	 * @return
-	 * @throws SQLException
-	 */
-	public List<WorkflowRun> getRuns(String dataflowID,
-			Map<String, String> conditions) throws SQLException {
-		List<WorkflowRun> result = new ArrayList<>();
-		StringBuilder q = new StringBuilder(
-				"SELECT * FROM WorkflowRun I join Workflow W on I.workflowId = W.workflowId");
-		List<String> conds = new ArrayList<>();
-		if (dataflowID != null)
-			conds.add("I.workflowId = '" + dataflowID + "'");
-		if (conditions != null) {
-			if (conditions.get("from") != null)
-				conds.add("timestamp >= " + conditions.get("from"));
-			if (conditions.get("to") != null)
-				conds.add("timestamp <= " + conditions.get("to"));
-		}
-		String sep = " where ";
-		for (String cond : conds) {
-			q.append(sep).append(cond);
-			sep = " and ";
-		}
-
-		q.append(" ORDER BY timestamp desc ");
-
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(q.toString())) {
-			logger.debug(q);
-			ResultSet rs = ps.executeQuery();
-			while (rs.next()) {
-				WorkflowRun i = new WorkflowRun();
-				i.setWorkflowRunId(rs.getString("workflowRunId"));
-				i.setTimestamp(rs.getString("timestamp"));
-				i.setWorkflowId(rs.getString("workflowId"));
-				i.setWorkflowExternalName(rs.getString("externalName"));
-				Blob blob = rs.getBlob("dataflow");
-				long length = blob.length();
-				blob.getBytes(1, (int) length);
-				i.setDataflowBlob(blob.getBytes(1, (int) length));
-				result.add(i);
-			}
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-
-	/**
-	 * @param constraints
-	 *            a Map columnName -> value that defines the query constraints.
-	 *            Note: columnName must be fully qualified. This is not done
-	 *            well at the moment, i.e., processorNameRef should be
-	 *            PortBinding.processorNameRef to avoid ambiguities
-	 * @return
-	 * @throws SQLException
-	 */
-	public List<PortBinding> getPortBindings(Map<String, String> constraints)
-			throws SQLException {
-		List<PortBinding> result = new ArrayList<>();
-
-		String q = "SELECT * FROM PortBinding VB "
-				+ "JOIN Port V ON VB.portName = V.portName "
-				+ "AND VB.processorNameRef = V.processorName "
-				+ "AND VB.workflowId = V.workflowId ";
-
-		try (Connection connection = getConnection();
-				Statement stmt = connection.createStatement();) {
-			ResultSet rs = stmt.executeQuery(addWhereClauseToQuery(q,
-					constraints, true));
-			while (rs.next()) {
-				PortBinding vb = new PortBinding();
-
-				vb.setWorkflowId(rs.getString("workflowId"));
-				vb.setPortName(rs.getString("portName"));
-				vb.setWorkflowRunId(rs.getString("workflowRunId"));
-				vb.setValue(rs.getString("value"));
-
-				if (rs.getString("collIdRef") == null || rs.getString("collIdRef").equals("null")) {
-					vb.setCollIDRef(null);
-				} else {
-					vb.setCollIDRef(rs.getString("collIdRef"));
-				}
-
-				vb.setIteration(rs.getString("iteration"));
-				vb.setProcessorName(rs.getString("processorNameRef"));
-				vb.setPositionInColl(rs.getInt("positionInColl"));
-				vb.setPortId(rs.getString("portId"));
-				vb.setIsInputPort(rs.getBoolean("isInputPort"));
-				result.add(vb);
-			}
-		} catch (Exception e) {
-			logger.warn("Add VB failed", e);
-		}
-		return result;
-	}
-
-	public List<NestedListNode> getNestedListNodes(
-			Map<String, String> constraints) throws SQLException {
-		List<NestedListNode> result = new ArrayList<>();
-
-		try (Connection connection = getConnection();
-				Statement stmt = connection.createStatement();
-				ResultSet rs = query("SELECT * FROM Collection C ").where(
-						constraints).exec(stmt)) {
-			while (rs.next()) {
-				NestedListNode nln = new NestedListNode();
-
-				nln.setCollectionT2Reference(rs.getString("collId"));
-				nln.setParentCollIdRef(rs.getString("parentCollIdRef"));
-				nln.setWorkflowRunId(rs.getString("workflowRunId"));
-				nln.setProcessorName(rs.getString("processorNameRef"));
-				nln.setPortName(rs.getString("portName"));
-				nln.setIteration(rs.getString("iteration"));
-
-				result.add(nln);
-			}
-		} catch (InstantiationException | IllegalAccessException
-				| ClassNotFoundException e) {
-			logger.error("Error finding the nested list nodes", e);
-		}
-		return result;
-	}
-
-	public Map<String, Integer> getPredecessorsCount(String workflowRunId) {
-		Map<String, Integer> result = new HashMap<>();
-
-		// get all datalinks for the entire workflow structure for this particular instance
-		try (Connection connection = getConnection()) {
-			PreparedStatement ps = connection
-					.prepareStatement("SELECT A.sourceProcessorName as source , A.destinationProcessorName as sink, A.workflowId as workflowId1, W1.workflowId as workflowId2, W2.workflowId as workflowId3 "
-							+ "FROM Datalink A join WorkflowRun I on A.workflowId = I.workflowId "
-							+ "left outer join Workflow W1 on W1.externalName = A.sourceProcessorName "
-							+ "left outer join Workflow W2 on W2.externalName = A.destinationProcessorName "
-							+ "where I.workflowRunId = ?");
-			ps.setString(1, workflowRunId);
-			ResultSet rs = ps.executeQuery();
-			while (rs.next()) {
-				String sink = rs.getString("sink");
-				String source = rs.getString("source");
-
-				if (result.get(sink) == null)
-					result.put(sink, 0);
-
-				String name1 = rs.getString("workflowId1");
-				String name2 = rs.getString("workflowId2");
-				String name3 = rs.getString("workflowId3");
-
-				if (isDataflow(source) && name1.equals(name2))
-					continue;
-				if (isDataflow(sink) && name1.equals(name3))
-					continue;
-
-				result.put(sink, result.get(sink) + 1);
-			}
-		} catch (InstantiationException | SQLException | IllegalAccessException | ClassNotFoundException e1) {
-			logger.warn("Could not execute query", e1);
-		}
-		return result;
-	}
-
-	/**
-	 * new impl of getProcessorsIncomingLinks whicih avoids complications due to nesting, and relies on the workflowRunId
-	 * rather than the workflowId
-	 * @param workflowRunId
-	 * @return
-	 */
-	public Map<String, Integer> getPredecessorsCountOld(String workflowRunId) {
-		Map<String, Integer> result = new HashMap<>();
-
-		// get all datalinks for the entire workflow structure for this particular instance
-		try (Connection connection = getConnection()) {
-			PreparedStatement ps = connection
-					.prepareStatement("SELECT destinationProcessorName, P1.firstActivityClass, count(*) as pred "
-							+ " FROM Datalink A join WorkflowRun I on A.workflowId = I.workflowId "
-							+ " join Processor P1 on P1.processorName = A.destinationProcessorName "
-							+ " join Processor P2 on P2.processorName = A.sourceProcessorName "
-							+ "  where I.workflowRunId = ? "
-							+ "  and P2.firstActivityClass <> '"
-							+ DATAFLOW_ACTIVITY
-							+ "' "
-							+ " and ((P1.firstActivityClass = '"
-							+ DATAFLOW_ACTIVITY
-							+ "'  and P1.workflowId = A.workflowId) or "
-							+ " (P1.firstActivityClass <> '"
-							+ DATAFLOW_ACTIVITY
-							+ "' )) "
-							+ " group by A.destinationProcessorName, firstActivityClass");
-			ps.setString(1, workflowRunId);
-			ResultSet rs = ps.executeQuery();
-			while (rs.next())
-				result.put(rs.getString("destinationProcessorName"),
-						new Integer(rs.getInt("pred")));
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException | SQLException e1) {
-			logger.warn("Could not execute query", e1);
-		}
-		return result;
-	}
-
-	/**
-	 * used in the toposort phase -- propagation of anl() values through the
-	 * graph
-	 *
-	 * @param workflowId
-	 *            reference to static wf name
-	 * @return a map <processor name> --> <incoming links count> for each
-	 *         processor, without counting the datalinks from the dataflow input to
-	 *         processors. So a processor is at the root of the graph if it has
-	 *         no incoming links, or all of its incoming links are from dataflow
-	 *         inputs.<br/>
-	 *         Note: this must be checked for processors that are roots of
-	 *         sub-flows... are these counted as top-level root nodes??
-	 */
-	public Map<String, Integer> getProcessorsIncomingLinks(String workflowId)
-			throws SQLException {
-		Map<String, Integer> result = new HashMap<>();
-
-		String currentWorkflowProcessor = null;
-		String sql = "SELECT processorName, firstActivityClass FROM Processor "
-				+ "WHERE workflowId = ?";
-
-		try (Connection c = getConnection()) {
-			try (PreparedStatement ps = c.prepareStatement(sql)) {
-				ps.setString(1, workflowId);
-				ResultSet rs = ps.executeQuery();
-				while (rs.next()) {
-					// PM CHECK 6/09
-					if (rs.getString("firstActivityClass").equals(
-							DATAFLOW_ACTIVITY)) {
-						currentWorkflowProcessor = rs
-								.getString("processorName");
-						logger.info("currentWorkflowProcessor = "
-								+ currentWorkflowProcessor);
-					}
-					result.put(rs.getString("processorName"), 0);
-				}
-			}
-
-			/*
-			 * fetch the name of the top-level dataflow. We use this to exclude
-			 * datalinks outgoing from its inputs
-			 */
-
-			// CHECK below -- gets confused on nested workflows
-			String parentWF = getParentOfWorkflow(workflowId);
-			if (parentWF == null)
-				parentWF = workflowId; // null parent means we are the top
-			logger.debug("parent WF: " + parentWF);
-
-			// get nested dataflows -- we want to avoid these in the toposort algorithm
-			List<ProvenanceProcessor> procs = getProcessorsShallow(c,
-					DATAFLOW_ACTIVITY, parentWF);
-
-			StringBuilder q = new StringBuilder("SELECT destinationProcessorName, count(*) AS cnt ");
-			q.append("FROM Datalink WHERE workflowId = \'").append(workflowId)
-					.append("\' AND destinationProcessorName NOT IN (");
-			String sep = "";
-			for (ProvenanceProcessor p : procs) {
-				q.append(sep).append("'").append(p.getProcessorName())
-						.append("'");
-				sep = ",";
-			}
-			q.append(") GROUP BY destinationProcessorName");
-
-			logger.info("executing \n" + q);
-
-			try (Statement stmt = c.createStatement();
-					ResultSet rs = stmt.executeQuery(q.toString())) {
-				while (rs.next())
-					if (!rs.getString("destinationProcessorName").equals(
-							currentWorkflowProcessor))
-						result.put(rs.getString("destinationProcessorName"),
-								rs.getInt("cnt"));
-				result.put(currentWorkflowProcessor, 0);
-			}
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-
-		return result;
-	}
-
-	public List<Port> getSuccPorts(String processorName, String portName,
-			String workflowId) throws SQLException {
-		List<Port> result = new ArrayList<>();
-		String sql = "SELECT v.* "
-				+ "FROM Datalink a JOIN Port v ON a.destinationProcessorName = v.processorName "
-				+ "AND  a.destinationPortName = v.portName "
-				+ "AND a.workflowId = v.workflowId "
-				+ "WHERE sourcePortName=? AND sourceProcessorName=?";
-		if (workflowId != null)
-			sql += " AND a.workflowId=?";
-
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(sql)) {
-			ps.setString(1, portName);
-			ps.setString(2, processorName);
-			if (workflowId != null)
-				ps.setString(3, workflowId);
-
-			ResultSet rs = ps.executeQuery();
-			while (rs.next()) {
-				Port aPort = new Port();
-
-				aPort.setWorkflowId(rs.getString("workflowId"));
-				aPort.setInputPort(rs.getBoolean("isInputPort"));
-				aPort.setIdentifier(rs.getString("portId"));
-				aPort.setProcessorName(rs.getString("processorName"));
-				aPort.setProcessorId(rs.getString("processorId"));
-				aPort.setPortName(rs.getString("portName"));
-				aPort.setDepth(rs.getInt("depth"));
-				if (rs.getString("resolvedDepth") != null)
-					aPort.setResolvedDepth(rs.getInt("resolvedDepth"));
-				result.add(aPort);
-			}
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-
-	public List<String> getSuccProcessors(String pName, String workflowId,
-			String workflowRunId) throws SQLException {
-		List<String> result = new ArrayList<>();
-		String sql = "SELECT distinct destinationProcessorName FROM Datalink A JOIN WorkflowRun I on A.workflowId = I.workflowId "
-				+ "WHERE A.workflowId = ? and I.workflowRunId = ? AND sourceProcessorName = ?";
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(sql)) {
-			ps.setString(1, workflowId);
-			ps.setString(2, workflowRunId);
-			ps.setString(3, pName);
-			ResultSet rs = ps.executeQuery();
-			while (rs.next())
-				result.add(rs.getString("destinationProcessorName"));
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-
-	/**
-	 * get all processors of a given type within a structure identified by
-	 * workflowId (reference to dataflow). type constraint is ignored if value is null.<br>
-	 * this only returns the processor for the input workflowId, without going into any neted workflows
-	 *
-	 * @param workflowId
-	 * @param firstActivityClass
-	 * @return a list, that contains at most one element
-	 * @throws SQLException
-	 */
-	public List<ProvenanceProcessor> getProcessorsShallow(
-			String firstActivityClass, String workflowId) throws SQLException {
-		Map<String, String> constraints = new HashMap<>();
-		constraints.put("P.workflowId", workflowId);
-		if (firstActivityClass != null)
-			constraints.put("P.firstActivityClass", firstActivityClass);
-		return getProcessors(constraints);
-	}
-
-	private List<ProvenanceProcessor> getProcessorsShallow(Connection c,
-			String firstActivityClass, String workflowId) throws SQLException {
-		Map<String, String> constraints = new HashMap<>();
-		constraints.put("P.workflowId", workflowId);
-		if (firstActivityClass != null)
-			constraints.put("P.firstActivityClass", firstActivityClass);
-		return getProcessors(c, constraints);
-	}
-
-	public ProvenanceProcessor getProvenanceProcessorByName(
-			String workflowId, String processorName) {
-		Map<String, String> constraints = new HashMap<>();
-		constraints.put("P.workflowId", workflowId);
-		constraints.put("P.processorName", processorName);
-		List<ProvenanceProcessor> processors;
-		try {
-			processors = getProcessors(constraints);
-		} catch (SQLException e1) {
-			logger.warn("Could not find processor for " + constraints, e1);
-			return null;
-		}
-		if (processors.size() != 1) {
-			logger.warn("Could not uniquely find processor for " + constraints + ", got: " + processors);
-			return null;
-		}
-		return processors.get(0);
-	}
-
-	public ProvenanceProcessor getProvenanceProcessorById(String processorId) {
-		Map<String, String> constraints = new HashMap<>();
-		constraints.put("P.processorId", processorId);
-		List<ProvenanceProcessor> processors;
-		try {
-			processors = getProcessors(constraints);
-		} catch (SQLException e1) {
-			logger.warn("Could not find processor for " + constraints, e1);
-			return null;
-		}
-		if (processors.size() != 1) {
-			logger.warn("Could not uniquely find processor for " + constraints
-					+ ", got: " + processors);
-			return null;
-		}
-		return processors.get(0);
-	}
-
-	/**
-	 * this is similar to {@link #getProcessorsShallow(String, String)} but it
-	 * recursively fetches all processors within nested workflows. The result is
-	 * collected in the form of a map: workflowId -> {ProvenanceProcessor}
-	 * 
-	 * @param firstActivityClass
-	 * @param workflowId
-	 * @return a map: workflowId -> {ProvenanceProcessor} where workflowId is
-	 *         the name of a (possibly nested) workflow, and the values are the
-	 *         processors within that workflow
-	 */
-	public Map<String, List<ProvenanceProcessor>> getProcessorsDeep(
-			String firstActivityClass, String workflowId) {
-		Map<String, List<ProvenanceProcessor>> result = new HashMap<>();
-
-		try {
-			List<ProvenanceProcessor> currentProcs = getProcessorsShallow(null,
-					workflowId);
-			List<ProvenanceProcessor> matchingProcessors = new ArrayList<>();
-			result.put(workflowId, matchingProcessors);
-			for (ProvenanceProcessor pp:currentProcs) {
-				if (firstActivityClass == null
-						|| pp.getFirstActivityClassName().equals(
-								firstActivityClass))
-					matchingProcessors.add(pp);
-				if (pp.getFirstActivityClassName().equals(DATAFLOW_ACTIVITY)) {
-					// Can't recurse as there's no way to find ID of nested workflow
-					continue;
-					//result.putAll(getProcessorsDeep(firstActivityClass, NESTED_WORKFLOW_ID));
-				}
-			}
-
-			// Silly fallback - use the broken getChildrenOfWorkflow() assuming that no other workflows
-			// have used the same nested workflow
-			for (String childWf : getChildrenOfWorkflow(workflowId))
-				result.putAll(getProcessorsDeep(firstActivityClass, childWf));
-		} catch (SQLException e) {
-			logger.error("Problem getting nested workflow processors for: " + workflowId, e);
-		}
-		return result;
-	}
-
-	public String getDataValue(String valueRef) {
-		String q = "SELECT * FROM Data where dataReference = ?;";
-
-		try (Connection connection = getConnection();
-				PreparedStatement stmt = connection.prepareStatement(q)) {
-			stmt.setString(1, valueRef);
-			ResultSet rs = stmt.executeQuery(q);
-			if (rs.next())
-				return rs.getString("data");
-		} catch (Exception e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	/**
-	 * generic method to fetch processors subject to additional query constraints
-	 * @param constraints
-	 * @return
-	 * @throws SQLException
-	 */
-	public List<ProvenanceProcessor> getProcessors(
-			Map<String, String> constraints) throws SQLException {
-		try (Connection connection = getConnection()) {
-			return getProcessors(connection, constraints);
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return new ArrayList<ProvenanceProcessor>();
-	}
-
-	private List<ProvenanceProcessor> getProcessors(Connection c,
-			Map<String, String> constraints) throws SQLException {
-		List<ProvenanceProcessor> result = new ArrayList<>();
-		try (Statement stmt = c.createStatement();
-				ResultSet rs = query("SELECT P.* FROM Processor P").where(
-						constraints).exec(stmt)) {
-			while (rs.next()) {
-				ProvenanceProcessor proc = new ProvenanceProcessor();
-				proc.setIdentifier(rs.getString("processorId"));
-				proc.setProcessorName(rs.getString("processorName"));
-				proc.setFirstActivityClassName(rs
-						.getString("firstActivityClass"));
-				proc.setWorkflowId(rs.getString("workflowId"));
-				proc.setTopLevelProcessor(rs.getBoolean("isTopLevel"));
-				result.add(proc);
-			}
-		}
-		return result;
-	}
-
-	public List<ProvenanceProcessor> getProcessorsForWorkflow(String workflowID) {
-		List<ProvenanceProcessor> result = new ArrayList<>();
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection
-						.prepareStatement("SELECT * from Processor WHERE workflowId=?")) {
-			ps.setString(1, workflowID);
-			ResultSet rs = ps.executeQuery();
-			while (rs.next()) {
-				ProvenanceProcessor proc = new ProvenanceProcessor();
-				proc.setIdentifier(rs.getString("processorId"));
-				proc.setProcessorName(rs.getString("processorName"));
-				proc.setFirstActivityClassName(rs
-						.getString("firstActivityClass"));
-				proc.setWorkflowId(rs.getString("workflowId"));
-				proc.setTopLevelProcessor(rs.getBoolean("isTopLevel"));
-				result.add(proc);
-			}
-		} catch (SQLException | InstantiationException | IllegalAccessException
-				| ClassNotFoundException e) {
-			logger.error("Problem getting processor for workflow: "
-					+ workflowID, e);
-		}
-		return result;
-	}
-
-	/**
-	 * simplest possible pinpoint query. Uses iteration info straight away. Assumes result is in PortBinding not in Collection
-	 *
-	 * @param workflowRun
-	 * @param pname
-	 * @param vname
-	 * @param iteration
-	 * @return
-	 */
-	public LineageSQLQuery simpleLineageQuery(String workflowRun, String workflowId, String pname,
-			String vname, String iteration) {
-		LineageSQLQuery lq = new LineageSQLQuery();
-		Q q = query("SELECT * FROM PortBinding VB "
-				+ "JOIN Port V ON (VB.portName = V.portName AND VB.processorNameRef = V.processorName AND VB.workflowId = V.workflowId) "
-				+ "JOIN WorkflowRun W ON VB.workflowRunId = W.workflowRunId AND VB.workflowId = W.workflowId ");
-
-		// constraints:
-		q.where("W.workflowRunId", workflowRun)
-				.where("VB.processorNameRef", pname)
-				.where("VB.workflowId", workflowId);
-
-		if (vname != null)
-			q.where("VB.portName", vname);
-		if (iteration != null)
-			q.where("VB.iteration", iteration);
-
-		// add order by clauses
-		q.orderBy("V.portName").orderBy("iteration");
-
-		logger.debug("Query is: " + q.query());
-		lq.setVbQuery(q.query());
-		return lq;
-	}
-
-	/**
-	 * if var2Path is null this generates a trivial query for the current output
-	 * var and current path
-	 *
-	 * @param workflowRunId
-	 * @param proc
-	 * @param var2Path
-	 * @param outputVar
-	 * @param path
-	 * @param returnOutputs
-	 *            returns inputs *and* outputs if set to true
-	 * @return
-	 */
-	public List<LineageSQLQuery> lineageQueryGen(String workflowRunId, String proc,
-			Map<Port, String> var2Path, Port outputVar, String path,
-			boolean returnOutputs) {
-		// setup
-		List<LineageSQLQuery> newQueries = new ArrayList<>();
-
-		// use the calculated path for each input var
-		boolean isInput = true;
-		for (Port v : var2Path.keySet()) {
-			LineageSQLQuery q = generateSQL2(workflowRunId, proc, v.getPortName(), var2Path.get(v), isInput);
-			if (q != null)
-				newQueries.add(q);
-		}
-
-		// is returnOutputs is true, then use proc, path for the output var as well
-		if (returnOutputs) {
-			isInput = false;
-			LineageSQLQuery q = generateSQL2(workflowRunId, proc, outputVar.getPortName(), path, isInput);  // && !var2Path.isEmpty());
-			if (q != null)
-				newQueries.add(q);
-		}
-		return newQueries;
-	}
-
-	protected LineageSQLQuery generateSQL2(String workflowRun, String proc,
-			String var, String path, boolean returnInput) {
-		LineageSQLQuery lq = new LineageSQLQuery();
-		Q q;
-
-		// base Collection query
-		q = query("SELECT C.*,W.workflowId,V.isInputPort FROM Collection C "
-				+ "JOIN WorkflowRun W ON C.workflowRunId = W.workflowRunId "
-				+ "JOIN Port V ON V.workflowId = W.workflowId "
-				+ "AND C.processorNameRef = V.processorName "
-				+ "AND C.portName = V.portName ");
-		if (path != null && path.length() > 0)
-			q.where("C.iteration", "[" + path + "]"); // PM 1/09 -- path
-		lq.setCollQuery(q.where("W.workflowRunId", workflowRun).where("C.processorNameRef",
-				proc).where("V.isInputPort", returnInput ? "1" : "0").query());
-
-		// base PortBinding query
-		q = query("SELECT VB.*,V.isInputPort FROM PortBinding VB "
-				+ "JOIN WorkflowRun W ON VB.workflowRunId = W.workflowRunId "
-				+ "JOIN Port V on V.workflowId = W.workflowId "
-				+ "AND VB.processorNameRef = V.processorName "
-				+ "AND VB.portName = V.portName ");
-		if (path != null && path.length() > 0)
-			q.where("VB.iteration", "[" + path + "]"); // PM 1/09 -- path
-		lq.setVbQuery(q.where("W.workflowRunId", workflowRun)
-				.where("VB.processorNameRef", proc).where("VB.portName", var)
-				.where("V.isInputPort", returnInput ? "1" : "0")
-				.orderBy("V.portName").orderBy("iteration").query());
-		return lq;
-	}
-
-	/**
-	 * if effectivePath is not null: query varBinding using: workflowRunId =
-	 * workflowRun, iteration = effectivePath, processorNameRef = proc if input vars is
-	 * null, then use the output var this returns the bindings for the set of
-	 * input vars at the correct iteration if effectivePath is null: fetch
-	 * PortBindings for all input vars, without constraint on the iteration<br/>
-	 * additionally, try querying the collection table first -- if the query succeeds, it means
-	 * the path is pointing to an internal node in the collection, and we just got the right node.
-	 * Otherwise, query PortBinding for the leaves
-	 *
-	 * @param workflowRun
-	 * @param proc
-	 * @param effectivePath
-	 * @param returnOutputs
-	 *            returns both inputs and outputs if set to true
-	 * @return
-	 */
-	public LineageSQLQuery generateSQL(String workflowRun, String proc,
-			String effectivePath, boolean returnOutputs) {
-		LineageSQLQuery lq = new LineageSQLQuery();
-		Q q;
-
-		// base Collection query
-		q = query("SELECT * FROM Collection C "
-				+ "JOIN WorkflowRun W ON C.workflowRunId = W.workflowRunId "
-				+ "JOIN Port V ON V.workflowRunId = W.workflowId "
-				+ "AND C.processorNameRef = V.processorNameRef "
-				+ "AND C.portName = V.portName ");
-
-		if (effectivePath != null && effectivePath.length() > 0)
-			q.where("C.iteration", "[" + effectivePath.toString() + "]"); // PM 1/09 -- path
-		// limit to inputs?
-		if (returnOutputs)
-			q.where("V.isInputPort", "1");
-
-		lq.setCollQuery(q.where("W.workflowRunId", workflowRun).where("C.processorNameRef",
-				proc).query());
-
-		// base PortBinding query
-		q = query("SELECT * FROM PortBinding VB "
-				+ "JOIN WorkflowRun W ON VB.workflowRunId = W.workflowRunId "
-				+ "JOIN Port V on V.workflowRunId = W.workflowId "
-				+ "AND VB.processorNameRef = V.processorNameRef "
-				+ "AND VB.portName = V.portName ");
-
-		if (effectivePath != null && effectivePath.length() > 0)
-			q.where("VB.iteration", "[" + effectivePath.toString() + "]"); // PM 1/09 -- path
-		// limit to inputs?
-		if (!returnOutputs)
-			q.where("V.isInputPort", "1");
-
-		lq.setVbQuery(q.where("W.workflowRunId", workflowRun)
-				.where("VB.processorNameRef", proc).orderBy("portName")
-				.orderBy("iteration").query());
-		return lq;
-	}
-
-	public Dependencies runCollectionQuery(LineageSQLQuery lq) throws SQLException {
-		String q = lq.getCollQuery();
-		Dependencies lqr = new Dependencies();
-		if (q == null)
-			return lqr;
-
-		logger.debug("running collection query: " + q);
-
-		try (Connection connection = getConnection();
-				Statement stmt = connection.createStatement()) {
-			ResultSet rs = stmt.executeQuery(q);
-			while (rs.next()) {
-				String type = Dependencies.ATOM_TYPE; // temp -- FIXME
-
-				String workflowId = rs.getString("workflowId");
-				String workflowRun = rs.getString("workflowRunId");
-				String proc = rs.getString("processorNameRef");
-				String var = rs.getString("portName");
-				String it = rs.getString("iteration");
-				String coll = rs.getString("collID");
-				String parentColl = rs.getString("parentCollIDRef");
-				//boolean isInput = rs.getBoolean("isInputPort");
-
-				lqr.addLineageQueryResultRecord(workflowId, proc, var, workflowRun,
-						it, coll, parentColl, null, null, type, false, true);  // true -> is a collection
-			}
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return lqr;
-	}
-
-	/**
-	 *
-	 * @param lq
-	 * @param includeDataValue  IGNORED. always false
-	 * @return
-	 * @throws SQLException
-	 */
-	public Dependencies runVBQuery(LineageSQLQuery lq, boolean includeDataValue)
-			throws SQLException {
-		String q = lq.getVbQuery();
-
-		logger.info("running VB query: " + q);
-
-		try (Connection connection = getConnection();
-				Statement stmt = connection.createStatement()) {
-			ResultSet rs = stmt.executeQuery(q);
-			Dependencies lqr = new Dependencies();
-
-			while (rs.next()) {
-				String type = Dependencies.ATOM_TYPE; // temp -- FIXME
-
-				String workflowId = rs.getString("workflowId");
-				String workflowRun = rs.getString("workflowRunId");
-				String proc = rs.getString("processorNameRef");
-				String var = rs.getString("portName");
-				String it = rs.getString("iteration");
-				String coll = rs.getString("collIDRef");
-				String value = rs.getString("value");
-				boolean isInput = rs.getBoolean("isInputPort");
-
-				// FIXME if the data is required then the query needs fixing
-				lqr.addLineageQueryResultRecord(workflowId, proc, var, workflowRun,
-						it, coll, null, value, null, type, isInput, false);
-			}
-			return lqr;
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	/**
-	 * executes one of the lineage queries produced by the graph visit algorithm. This first executes the collection query, and then
-	 * if no result is returned, the varBinding query
-	 *
-	 * @param lq
-	 *            a lineage query computed during the graph traversal
-	 * @param includeDataValue
-	 *            if true, then the referenced value is included in the result.
-	 *            This may only be necessary for testing: the data reference in
-	 *            field value (which is a misleading field name, and actually
-	 *            refers to the data reference) should be sufficient
-	 * @return
-	 * @throws SQLException
-	 */
-	public Dependencies runLineageQuery(LineageSQLQuery lq,
-			boolean includeDataValue) throws SQLException {
-		Dependencies result = runCollectionQuery(lq);
-		if (result.getRecords().isEmpty())
-			return runVBQuery(lq, includeDataValue);
-		return result;
-	}
-
-	public List<Dependencies> runLineageQueries(List<LineageSQLQuery> lqList,
-			boolean includeDataValue) throws SQLException {
-		List<Dependencies> allResults = new ArrayList<>();
-		if (lqList == null)
-			logger.warn("lineage queries list is NULL, nothing to evaluate");
-		else
-			for (LineageSQLQuery lq : lqList)
-				if (lq != null)
-					allResults.add(runLineageQuery(lq, includeDataValue));
-		return allResults;
-	}
-
-	/**
-	 * takes an ordered set of records for the same variable with iteration
-	 * indexes and builds a collection out of it
-	 *
-	 * @param lqr
-	 * @return a jdom Document with the collection
-	 */
-	public Document recordsToCollection(Dependencies lqr) {
-		// process each var name in turn
-		// lqr ordered by var name and by iteration number
-		Document d = new Document(new Element("list"));
-
-		String currentVar = null;
-		for (ListIterator<LineageQueryResultRecord> it = lqr.iterator(); it.hasNext();) {
-			LineageQueryResultRecord record = it.next();
-
-			if (currentVar != null && record.getPortName().equals(currentVar)) {
-				// multiple occurrences
-				addToCollection(record, d);
-				// adds record to d in the correct position given by the iteration vector
-			}
-			if (currentVar == null)
-				currentVar = record.getPortName();
-		}
-		return d;
-	}
-
-	private void addToCollection(LineageQueryResultRecord record, Document d) {
-		Element root = d.getRootElement();
-		String[] itVector = record.getIteration().split(",");
-		Element currentEl = root;
-		// each element gives us a corresponding child in the tree
-		for (int i = 0; i < itVector.length; i++) {
-			int index = Integer.parseInt(itVector[i]);
-			List<?> children = currentEl.getChildren();
-			if (index < children.size())
-				currentEl = (Element) children.get(index);
-			else if (i == itVector.length - 1)
-				currentEl.addContent(new Element(record.getValue()));
-			else
-				currentEl.addContent(new Element("list"));
-		}
-	}
-
-	/**
-	 *
-	 * returns the set of all processors that are structurally contained within
-	 * the wf corresponding to the input dataflow name
-	 * @param workflowName the name of a processor of type DataFlowActivity
-	 * @return
-	 *
-	 * @deprecated as workflow 'names' are not globally unique, this method should not be used!
-	 */
-	@Deprecated
-	public List<String> getContainedProcessors(String workflowName) {
-		List<String> result = new ArrayList<>();
-
-		// dataflow name -> wfRef
-		String containerDataflow = getWorkflowIdForExternalName(workflowName);
-
-		// get all processors within containerDataflow
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection
-						.prepareStatement("SELECT processorName FROM Processor P "
-								+ "WHERE workflowId = ?")) {
-			ps.setString(1, containerDataflow);
-			ResultSet rs = ps.executeQuery();
-			while (rs.next())
-				result.add(rs.getString("processorName"));
-		} catch (InstantiationException | SQLException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-
-	public String getTopLevelDataflowName(String workflowRunId) {
-		String sql = "SELECT processorName FROM Processor P "
-				+ "JOIN WorkflowRun I on P.workflowId = I.workflowId "
-				+ "WHERE I.workflowRunId = ? AND isTopLevel = 1";
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(sql)) {
-			ps.setString(1, workflowRunId);
-			ResultSet rs = ps.executeQuery();
-			if (rs.next())
-				return rs.getString("processorName");
-		} catch (InstantiationException | SQLException | IllegalAccessException
-				| ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	/**
-	 * retrieve a tree structure starting from the top parent
-	 * @param workflowID
-	 * @return
-	 * @throws SQLException
-	 */
-	public WorkflowTree getWorkflowNestingStructure(String workflowID) throws SQLException {
-		WorkflowTree tree = new WorkflowTree();
-
-	    Workflow wf = getWorkflow(workflowID);
-	    tree.setNode(wf);
-
-	    List<String> children = getChildrenOfWorkflow(workflowID);
-	    for (String childWfName:children) {
-	    	WorkflowTree childStructure = getWorkflowNestingStructure(childWfName);
-	    	tree.addChild(childStructure);
-	    }
-	    return tree;
-	}
-
-	/**
-	 * returns the internal ID of a dataflow given its external name
-	 * @param externalName
-	 * @param workflowRunId
-	 * @return
-	 * @deprecated as workflow 'names' are not globally unique, this method should not be used!
-	 */
-	@Deprecated
-	public String getWorkflowIdForExternalName(String externalName) {
-		//"SELECT workflowId FROM Workflow W join WorkflowRun I on W.workflowId = I.workflowId WHERE W.externalName = ? and I.workflowRunId = ?");
-		String sql = "SELECT workflowId FROM Workflow W WHERE W.externalName = ?";
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(sql)) {
-			ps.setString(1, externalName);
-			// ps.setString(2, workflowRunId);
-			ResultSet rs = ps.executeQuery();
-			if (rs.next())
-				return rs.getString("workflowId");
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException | SQLException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	/**
-	 * This method is deprecated as parent workflow ID is not correctly
-	 * recorded. If two workflows both contain the same nested workflow, only
-	 * one of them (the most recently added) will return that nested workflow
-	 * from this method.
-	 *
-	 * @deprecated
-	 * @param parentWorkflowId
-	 * @return
-	 * @throws SQLException
-	 */
-	@Deprecated
-	public List<String> getChildrenOfWorkflow(String parentWorkflowId)
-			throws SQLException {
-		List<String> result = new ArrayList<>();
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection
-						.prepareStatement("SELECT workflowId FROM Workflow WHERE parentWorkflowId = ? ")) {
-			ps.setString(1, parentWorkflowId);
-			ResultSet rs = ps.executeQuery();
-			while (rs.next())
-				result.add(rs.getString("workflowId"));
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-
-	/**
-	 * fetch children of parentWorkflowId from the Workflow table
-	 *
-	 * @return
-	 * @param childworkflowId
-	 * @throws SQLException
-	 */
-	public String getParentOfWorkflow(String childworkflowId)
-			throws SQLException {
-		String result = null;
-		String q = "SELECT parentWorkflowId FROM Workflow WHERE workflowId = ?";
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(q)) {
-			ps.setString(1, childworkflowId);
-
-			logger.debug("getParentOfWorkflow - query: " + q
-					+ "  with workflowId = " + childworkflowId);
-
-			ResultSet rs = ps.executeQuery();
-			while (rs.next()) {
-				result = rs.getString("parentWorkflowId");
-				logger.debug("result: " + result);
-				break;
-			}
-		} catch (InstantiationException | IllegalAccessException
-				| ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-
-	public List<String> getAllworkflowIds() throws SQLException {
-		List<String> result = new ArrayList<>();
-		String q = "SELECT workflowId FROM Workflow";
-		try (Connection connection = getConnection();
-				Statement stmt = connection.createStatement()) {
-			ResultSet rs = stmt.executeQuery(q);
-			while (rs.next())
-				result.add(rs.getString("workflowId"));
-		} catch (InstantiationException | IllegalAccessException
-				| ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-
-	/**
-	 * @deprecated This method is not workflowId aware and should not be used
-	 * @param procName
-	 * @return true if procName is the external name of a dataflow, false
-	 *         otherwise
-	 * @throws SQLException
-	 */
-	public boolean isDataflow(String procName) throws SQLException {
-		String sql = "SELECT firstActivityClass FROM Processor WHERE processorName = ?";
-		try (Connection c = getConnection();
-				PreparedStatement ps = c.prepareStatement(sql)) {
-			ps.setString(1, procName);
-			ResultSet rs = ps.executeQuery();
-			if (rs.next()
-					&& DATAFLOW_ACTIVITY.equals(rs
-							.getString("firstActivityClass")))
-				return true;
-		} catch (InstantiationException | IllegalAccessException
-				| ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return false;
-	}
-
-	public boolean isTopLevelDataflow(String workflowIdID) {
-		String sql = "SELECT * FROM Workflow W where W.workflowId = ?";
-		try (Connection c = getConnection();
-				PreparedStatement ps = c.prepareStatement(sql)) {
-			ps.setString(1, workflowIdID);
-			ResultSet rs = ps.executeQuery();
-			if (rs.next())
-				return (rs.getString("parentWorkflowId") == null);
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return false;
-	}
-
-	public boolean isTopLevelDataflow(String workflowId, String workflowRunId) {
-		String sql = "SELECT " + parentProcessorEnactmentId + " AS parent"
-				+ " FROM " + DataflowInvocation + " W " + " WHERE "
-				+ DataflowInvocationTable.workflowId + "=? AND "
-				+ DataflowInvocationTable.workflowRunId + "=?";
-		try (Connection c = getConnection();
-				PreparedStatement ps = c.prepareStatement(sql)) {
-			ps.setString(1, workflowId);
-			ps.setString(2, workflowRunId);
-			ResultSet rs = ps.executeQuery();
-			if (rs.next())
-				return (rs.getString("parent") == null);
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return false;
-	}
-
-	public String getTopDataflow(String workflowRunId) {
-		String sql = "SELECT processorName FROM "
-				+ "Processor P JOIN WorkflowRun I ON P.workflowId = I.workflowId "
-				+ " WHERE I.workflowRunId = ? AND isTopLevel = 1 ";
-		try (Connection c = getConnection();
-				PreparedStatement ps = c.prepareStatement(sql)) {
-			ps.setString(1, workflowRunId);
-			ResultSet rs = ps.executeQuery();
-			if (rs.next())
-				return rs.getString("processorName");
-		} catch (SQLException | InstantiationException | IllegalAccessException
-				| ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	/**
-	 *
-	 * @param p
-	 *            pTo processor
-	 * @param var
-	 *            vTo
-	 * @param value
-	 *            valTo
-	 * @return a set of DDRecord
-	 * @throws SQLException
-	 */
-	public List<DDRecord> queryDD(String p, String var, String value,
-			String iteration, String workflowRun) throws SQLException {
-		Q q = query("SELECT * FROM DD ");
-		q.where("pTo", p);
-		q.where("vTo", var);
-		if (value != null)
-			q.where("valTo", value);
-		if (iteration != null)
-			q.where("iteration", iteration);
-		if (workflowRun != null)
-			q.where("workflowRun", workflowRun);
-
-		try (Connection connection = getConnection();
-				Statement stmt = connection.createStatement();
-				ResultSet rs = q.exec(stmt)) {
-			List<DDRecord> result = new ArrayList<>();
-			while (rs.next()) {
-				DDRecord aDDrecord = new DDRecord();
-				aDDrecord.setPFrom(rs.getString("pFrom"));
-				aDDrecord.setVFrom(rs.getString("vFrom"));
-				aDDrecord.setValFrom(rs.getString("valFrom"));
-				aDDrecord.setPTo(rs.getString("pTo"));
-				aDDrecord.setVTo(rs.getString("vTo"));
-				aDDrecord.setValTo(rs.getString("valTo"));
-				result.add(aDDrecord);
-			}
-			return result;
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	public Set<DDRecord> queryDataLinksForDD(String p, String v, String val,
-			String workflowRun) throws SQLException {
-		String sql = "SELECT DISTINCT A.sourceProcessorName AS p, A.sourcePortName AS var, VB.value AS val "
-				+ "FROM   Datalink A "
-				+ "JOIN   PortBinding VB ON VB.portName = A.destinationPortName AND VB.processorNameRef = A.destinationProcessorName "
-				+ "JOIN   WorkflowRun WF ON WF.workflowId = A.workflowId AND WF.workflowRunId = VB.workflowRunId  "
-				+ "WHERE  WF.workflowRunId = ? AND A.destinationProcessorName = ? AND A.destinationPortName = ? AND VB.value = ?";
-
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(sql)) {
-			ps.setString(1, workflowRun);
-			ps.setString(2, p);
-			ps.setString(3, v);
-			ps.setString(4, val);
-			ResultSet rs = ps.executeQuery();
-			Set<DDRecord> result = new HashSet<>();
-			while (rs.next()) {
-				DDRecord aDDrecord = new DDRecord();
-				aDDrecord.setPTo(rs.getString("p"));
-				aDDrecord.setVTo(rs.getString("var"));
-				aDDrecord.setValTo(rs.getString("val"));
-				result.add(aDDrecord);
-			}
-			return result;
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	public Set<DDRecord> queryAllFromValues(String workflowRun)
-			throws SQLException {
-		String sql = "SELECT DISTINCT PFrom, vFrom, valFrom FROM DD where workflowRun = ?";
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(sql)) {
-			ps.setString(1, workflowRun);
-			ResultSet rs = ps.executeQuery();
-			Set<DDRecord> result = new HashSet<>();
-			while (rs.next()) {
-				DDRecord aDDrecord = new DDRecord();
-				aDDrecord.setPFrom(rs.getString("PFrom"));
-				aDDrecord.setVFrom(rs.getString("vFrom"));
-				aDDrecord.setValFrom(rs.getString("valFrom"));
-				result.add(aDDrecord);
-			}
-			return result;
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query", e);
-			return null;
-		}
-	}
-
-	public boolean isRootProcessorOfWorkflow(String procName, String workflowId,
-			String workflowRunId) {
-		String sql = "SELECT * FROM Datalink A JOIN WorkflowRun I ON A.workflowId = I.workflowId "
-				+ "JOIN Processor P on P.processorName = A.sourceProcessorName "
-				+ "WHERE sourceProcessorName = ? "
-				+ "AND P.workflowId <> A.workflowId "
-				+ "AND I.workflowRunId = ? "
-				+ "AND destinationProcessorName = ? ";
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(sql)) {
-			ps.setString(1, workflowId);
-			ps.setString(2, workflowRunId);
-			ps.setString(3, procName);
-			if (ps.executeQuery().next())
-				return true;
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException | SQLException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return false;
-	}
-
-	/**
-	 * returns a Workflow record from the DB given the workflow internal ID
-	 * @param dataflowID
-	 * @return
-	 */
-	public Workflow getWorkflow(String dataflowID) {
-		String sql = "SELECT * FROM Workflow W WHERE workflowId = ? ";
-		try (Connection connection = getConnection();
-				PreparedStatement ps = connection.prepareStatement(sql)) {
-			ps.setString(1, dataflowID);
-			ResultSet rs = ps.executeQuery();
-			if (rs.next()) {
-				Workflow wf = new Workflow();
-				wf.setWorkflowId(rs.getString("workflowId"));
-				wf.setParentWorkflowId(rs.getString("parentWorkflowId"));
-				wf.setExternalName(rs.getString("externalName"));
-
-				return wf;
-			} else {
-				logger.warn("Could not find workflow " + dataflowID);
-			}
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException | SQLException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	/**
-	 * @param record
-	 *            a record representing a single value -- possibly within a list
-	 *            hierarchy
-	 * @return the URI for topmost containing collection when the input record
-	 *         is within a list hierarchy, or null otherwise
-	 */
-	public String getContainingCollection(LineageQueryResultRecord record) {
-		if (record.getCollectionT2Reference() == null)
-			return null;
-		String sql = "SELECT * FROM Collection "
-				+ "WHERE collID = ? and workflowRunId = ? and processorNameRef = ? and portName = ?";
-		try (Connection connection = getConnection()) {
-			String parentCollIDRef = null;
-			try (PreparedStatement stmt = connection.prepareStatement(sql)) {
-				stmt.setString(1, record.getCollectionT2Reference());
-				stmt.setString(2, record.getWorkflowRunId());
-				stmt.setString(3, record.getProcessorName());
-				stmt.setString(4, record.getPortName());
-				ResultSet rs = stmt.executeQuery();
-				if (rs.next())
-					parentCollIDRef = rs.getString("parentCollIDRef");
-			}
-
-			// INITIALLY not null -- would be TOP if the initial had no parent
-			while (parentCollIDRef != null) {
-				String oldParentCollIDRef = parentCollIDRef;
-
-				// query Collection again for parent collection
-				try (PreparedStatement stmt = connection.prepareStatement(sql)) {
-					stmt.setString(1, oldParentCollIDRef);
-					stmt.setString(2, record.getWorkflowRunId());
-					stmt.setString(3, record.getProcessorName());
-					stmt.setString(4, record.getPortName());
-					ResultSet rs = stmt.executeQuery();
-					if (rs.next()) {
-						parentCollIDRef = rs.getString("parentCollIDRef");
-						if (parentCollIDRef.equals("TOP"))
-							return oldParentCollIDRef;
-					}
-				} catch (Exception e) {
-					logger.warn("Could not execute query", e);
-				}
-			}
-		} catch (InstantiationException | IllegalAccessException | ClassNotFoundException | SQLException e) {
-			logger.warn("Could not execute query", e);
-		}
-		return null;
-	}
-
-	public List<ProcessorEnactment> getProcessorEnactments(
-			String workflowRunId, String... processorPath) {
-		return getProcessorEnactments(workflowRunId,
-				(List<ProcessorEnactment>) null, Arrays.asList(processorPath));
-	}
-
-	private List<ProcessorEnactment> getProcessorEnactments(
-			String workflowRunId, List<ProcessorEnactment> parentProcessorEnactments,
-			List<String> processorPath) {
-		List<String> processorEnactmentIds = null;
-		if (parentProcessorEnactments != null) {
-			processorEnactmentIds = new ArrayList<>();
-			for (ProcessorEnactment processorEnactment : parentProcessorEnactments)
-				processorEnactmentIds.add(processorEnactment.getProcessEnactmentId());
-		}
-		if (processorPath.size() > 1) {
-			return getProcessorEnactments(
-					workflowRunId,
-					getProcessorEnactmentsByProcessorName(workflowRunId,
-							processorEnactmentIds, processorPath.get(0)),
-					processorPath.subList(1, processorPath.size()));
-		} else if (processorPath.size() == 1) {
-			return getProcessorEnactmentsByProcessorName(workflowRunId,
-					processorEnactmentIds, processorPath.get(0));
-		} else {
-			return getProcessorEnactmentsByProcessorName(workflowRunId,
-					processorEnactmentIds, null);
-		}
-	}
-
-	public List<ProcessorEnactment> getProcessorEnactmentsByProcessorName(
-			String workflowRunId, List<String> parentProcessorEnactmentIds,
-			String processorName) {
-		StringBuilder query = new StringBuilder();
-		query.append("SELECT ")
-				.append(ProcessorEnactmentTable.enactmentStarted).append(", ")
-				.append(ProcessorEnactmentTable.enactmentEnded).append(", ")
-				.append(ProcessorEnactmentTable.finalOutputsDataBindingId)
-				.append(", ")
-				.append(ProcessorEnactmentTable.initialInputsDataBindingId)
-				.append(", ")
-				.append(ProcessorEnactmentTable.ProcessorEnactment).append(".")
-				.append(ProcessorEnactmentTable.processorId)
-				.append(" AS procId, ")
-				.append(ProcessorEnactmentTable.processIdentifier).append(", ")
-				.append(ProcessorEnactmentTable.processEnactmentId)
-				.append(", ")
-				.append(ProcessorEnactmentTable.parentProcessorEnactmentId)
-				.append(", ").append(ProcessorEnactmentTable.workflowRunId)
-				.append(", ").append(ProcessorEnactmentTable.iteration)
-				.append(", Processor.processorName FROM ")
-				.append(ProcessorEnactmentTable.ProcessorEnactment)
-				.append(" INNER JOIN Processor ON ")
-				.append(ProcessorEnactmentTable.ProcessorEnactment).append(".")
-				.append(ProcessorEnactmentTable.processorId)
-				.append(" = Processor.processorId WHERE ")
-				.append(ProcessorEnactmentTable.workflowRunId).append(" = ? ");
-
-		if (processorName != null)
-			// Specific processor
-			query.append(" AND Processor.processorName = ? ");
-		if ((parentProcessorEnactmentIds == null || parentProcessorEnactmentIds.isEmpty()) && processorName != null) {
-			// null - ie. top level
-			query.append(" AND " + ProcessorEnactmentTable.parentProcessorEnactmentId + " IS NULL");
-		} else if (parentProcessorEnactmentIds != null) {
-			// not null, ie. inside nested workflow
-			query.append(" AND " + ProcessorEnactmentTable.parentProcessorEnactmentId + " IN (");
-			for (int i=0; i<parentProcessorEnactmentIds.size(); i++) {
-				query.append('?');
-				if (i < (parentProcessorEnactmentIds.size()-1))
-					query.append(',');
-			}
-			query.append(')');
-		}
-
-		ArrayList<ProcessorEnactment> procEnacts = new ArrayList<>();
-
-		try (Connection connection = getConnection();
-				PreparedStatement statement = connection.prepareStatement(query
-						.toString())) {
-			int pos = 1;
-			statement.setString(pos++, workflowRunId);
-			if (processorName != null)
-				statement.setString(pos++, processorName);
-			if (parentProcessorEnactmentIds != null)
-				for (String parentId : parentProcessorEnactmentIds)
-					statement.setString(pos++, parentId);
-			ResultSet resultSet = statement.executeQuery();
-			while (resultSet.next()) {
-				ProcessorEnactment procEnact = readProcessorEnactment(resultSet);
-				procEnacts.add(procEnact);
-			}
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query " + query, e);
-		}
-		return procEnacts;
-	}
-
-	private ProcessorEnactment readProcessorEnactment(ResultSet resultSet) throws SQLException {
-		Timestamp enactmentStarted = resultSet.getTimestamp(ProcessorEnactmentTable.enactmentStarted.name());
-		Timestamp enactmentEnded = resultSet.getTimestamp(ProcessorEnactmentTable.enactmentEnded.name());
-		//String pName = resultSet.getString("processorName");
-		String finalOutputsDataBindingId = resultSet.getString(ProcessorEnactmentTable.finalOutputsDataBindingId.name());
-		String initialInputsDataBindingId = resultSet.getString(ProcessorEnactmentTable.initialInputsDataBindingId.name());
-
-		String iteration = resultSet.getString(ProcessorEnactmentTable.iteration.name());
-		String processorId = resultSet.getString("procId");
-		String processIdentifier = resultSet.getString(ProcessorEnactmentTable.processIdentifier.name());
-		String processEnactmentId = resultSet.getString(ProcessorEnactmentTable.processEnactmentId.name());
-		String parentProcessEnactmentId = resultSet.getString(ProcessorEnactmentTable.parentProcessorEnactmentId.name());
-		String workflowRunId = resultSet.getString(ProcessorEnactmentTable.workflowRunId.name());
-
-		ProcessorEnactment procEnact = new ProcessorEnactment();
-		procEnact.setEnactmentEnded(enactmentEnded);
-		procEnact.setEnactmentStarted(enactmentStarted);
-		procEnact.setFinalOutputsDataBindingId(finalOutputsDataBindingId);
-		procEnact.setInitialInputsDataBindingId(initialInputsDataBindingId);
-		procEnact.setIteration(iteration);
-		procEnact.setParentProcessorEnactmentId(parentProcessEnactmentId);
-		procEnact.setProcessEnactmentId(processEnactmentId);
-		procEnact.setProcessIdentifier(processIdentifier);
-		procEnact.setProcessorId(processorId);
-		procEnact.setWorkflowRunId(workflowRunId);
-		return procEnact;
-	}
-
-	public ProcessorEnactment getProcessorEnactment(String processorEnactmentId) {
-		String query  =
-				"SELECT " + ProcessorEnactmentTable.enactmentStarted + ","
-						+ ProcessorEnactmentTable.enactmentEnded + ","
-						+ ProcessorEnactmentTable.finalOutputsDataBindingId + ","
-						+ ProcessorEnactmentTable.initialInputsDataBindingId + ","
-						+ ProcessorEnactmentTable.ProcessorEnactment + "."
-						+ ProcessorEnactmentTable.processorId + " AS procId,"
-						+ ProcessorEnactmentTable.processIdentifier + ","
-						+ ProcessorEnactmentTable.workflowRunId + ","
-						+ ProcessorEnactmentTable.processEnactmentId + ","
-						+ ProcessorEnactmentTable.parentProcessorEnactmentId + ","
-						+ ProcessorEnactmentTable.iteration
-						+ " FROM "
-						+ ProcessorEnactmentTable.ProcessorEnactment
-						+ " WHERE "
-						+ ProcessorEnactmentTable.processEnactmentId + "=?";
-
-		ProcessorEnactment procEnact = null;
-		try (Connection connection = getConnection();
-				PreparedStatement statement = connection
-						.prepareStatement(query)) {
-			statement.setString(1, processorEnactmentId);
-			ResultSet resultSet = statement.executeQuery();
-			if (!resultSet.next()) {
-				logger.warn("Could not find ProcessorEnactment processEnactmentId="
-						+ processorEnactmentId);
-				return null;
-			}
-			procEnact = readProcessorEnactment(resultSet);
-			if (resultSet.next()) {
-				logger.error("Found more than one ProcessorEnactment processEnactmentId="
-						+ processorEnactmentId);
-				return null;
-			}
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query " + query, e);
-		}
-		return procEnact;
-	}
-
-	public ProcessorEnactment getProcessorEnactmentByProcessId(
-			String workflowRunId, String processIdentifier, String iteration) {
-		String query = "SELECT " + ProcessorEnactmentTable.enactmentStarted
-				+ "," + ProcessorEnactmentTable.enactmentEnded + ","
-				+ ProcessorEnactmentTable.finalOutputsDataBindingId + ","
-				+ ProcessorEnactmentTable.initialInputsDataBindingId + ","
-				+ ProcessorEnactmentTable.ProcessorEnactment + "."
-				+ ProcessorEnactmentTable.processorId + " AS procId,"
-				+ ProcessorEnactmentTable.processIdentifier + ","
-				+ ProcessorEnactmentTable.workflowRunId + ","
-				+ ProcessorEnactmentTable.processEnactmentId + ","
-				+ ProcessorEnactmentTable.parentProcessorEnactmentId + ","
-				+ ProcessorEnactmentTable.iteration + " FROM "
-				+ ProcessorEnactmentTable.ProcessorEnactment + " WHERE "
-				+ ProcessorEnactmentTable.workflowRunId + "=?" + " AND "
-				+ ProcessorEnactmentTable.processIdentifier + "=?" + " AND "
-				+ ProcessorEnactmentTable.iteration + "=?";
-
-		ProcessorEnactment procEnact = null;
-		try (Connection connection = getConnection();
-				PreparedStatement statement = connection
-						.prepareStatement(query)) {
-			statement.setString(1, workflowRunId);
-			statement.setString(2, processIdentifier);
-			statement.setString(3, iteration);
-
-			ResultSet resultSet = statement.executeQuery();
-			String debugString = "ProcessorEnactment runId=" + workflowRunId
-					+ " processIdentifier=" + processIdentifier + " iteration="
-					+ iteration;
-			if (!resultSet.next()) {
-				logger.warn("Could not find " + debugString);
-				return null;
-			}
-			procEnact = readProcessorEnactment(resultSet);
-			if (resultSet.next()) {
-				logger.error("Found more than one " + debugString);
-				return null;
-			}
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query " + query, e);
-		}
-		return procEnact;
-	}
-
-	public Map<Port, String> getDataBindings(String dataBindingId) {
-		HashMap<Port, String> dataBindings = new HashMap<>();
-		String query = "SELECT " + DataBindingTable.t2Reference + ","
-				+ "Port.portId AS portId," + "Port.processorName,"
-				+ "Port.processorId," + "Port.isInputPort," + "Port.portName,"
-				+ "Port.depth," + "Port.resolvedDepth," + "Port.workflowId"
-				+ " FROM " + DataBindingTable.DataBinding + " INNER JOIN "
-				+ "Port" + " ON " + " Port.portId="
-				+ DataBindingTable.DataBinding + "." + DataBindingTable.portId
-				+ " WHERE " + DataBindingTable.dataBindingId + "=?";
-		try (Connection connection = getConnection();
-				PreparedStatement statement = connection
-						.prepareStatement(query)) {
-			statement.setString(1, dataBindingId);
-			ResultSet rs = statement.executeQuery();
-			while (rs.next()) {
-				String t2Ref = rs.getString(DataBindingTable.t2Reference.name());
-
-				Port port = new Port();
-				port.setWorkflowId(rs.getString("workflowId"));
-				port.setInputPort(rs.getBoolean("isInputPort"));
-				port.setIdentifier(rs.getString("portId"));
-				port.setProcessorName(rs.getString("processorName"));
-				port.setProcessorId(rs.getString("processorId"));
-				port.setPortName(rs.getString("portName"));
-				port.setDepth(rs.getInt("depth"));
-				if (rs.getString("resolvedDepth") != null)
-					port.setResolvedDepth(rs.getInt("resolvedDepth"));
-				dataBindings.put(port, t2Ref);
-			}
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query " + query, e);
-		}
-		return dataBindings;
-	}
-
-	public List<Port> getAllPortsInDataflow(String workflowID) {
-		Map<String, String> queryConstraints = new HashMap<>();
-		queryConstraints.put("V.workflowId", workflowID);
-		try {
-			return getPorts(queryConstraints);
-		} catch (SQLException e) {
-			logger.error("Problem getting ports for dataflow: " + workflowID, e);
-			return null;
-		}
-	}
-
-	public List<Port> getPortsForDataflow(String workflowID) {
-		Workflow w = getWorkflow(workflowID);
-
-		Map<String, String> queryConstraints = new HashMap<>();
-		queryConstraints.put("V.workflowId", workflowID);
-		queryConstraints.put("processorName", w.getExternalName());
-
-		try {
-			return getPorts(queryConstraints);
-		} catch (SQLException e) {
-			logger.error("Problem getting ports for dataflow: " + workflowID, e);
-			return null;
-		}
-	}
-
-	public List<Port> getPortsForProcessor(String workflowID,
-			String processorName) {
-		Map<String, String> queryConstraints = new HashMap<>();
-		queryConstraints.put("V.workflowId", workflowID);
-		queryConstraints.put("processorName", processorName);
-
-		try {
-			return getPorts(queryConstraints);
-		} catch (SQLException e) {
-			logger.error("Problem getting ports for processor: "
-					+ processorName + " worflow: " + workflowID, e);
-			return null;
-		}
-	}
-
-	public DataflowInvocation getDataflowInvocation(String workflowRunId) {
-		String query = "SELECT " +
-				  DataflowInvocationTable.dataflowInvocationId + ","
-				+ DataflowInvocationTable.inputsDataBinding + ","
-				+ DataflowInvocationTable.invocationEnded + ","
-				+ DataflowInvocationTable.invocationStarted + ","
-				+ DataflowInvocationTable.outputsDataBinding + ","
-				+ DataflowInvocationTable.parentProcessorEnactmentId + ","
-				+ DataflowInvocationTable.workflowId + ","
-				+ DataflowInvocationTable.workflowRunId + ","
-				+ DataflowInvocationTable.completed
-				+ " FROM "
-				+ DataflowInvocationTable.DataflowInvocation +
-				" WHERE "
-				+ DataflowInvocationTable.parentProcessorEnactmentId + " IS NULL AND "
-				+ DataflowInvocationTable.workflowRunId + "=?";
-		DataflowInvocation dataflowInvocation = null;
-		try (Connection connection = getConnection();
-				PreparedStatement statement = connection
-						.prepareStatement(query)) {
-			statement.setString(1, workflowRunId);
-			ResultSet rs = statement.executeQuery();
-			if (!rs.next()) {
-				logger.warn("Could not find DataflowInvocation for workflowRunId=" + workflowRunId);
-				return null;
-			}
-			dataflowInvocation = new DataflowInvocation();
-			dataflowInvocation.setDataflowInvocationId(rs.getString(DataflowInvocationTable.dataflowInvocationId.name()));
-			dataflowInvocation.setInputsDataBindingId(rs.getString(DataflowInvocationTable.inputsDataBinding.name()));
-			dataflowInvocation.setInvocationEnded(rs.getTimestamp(DataflowInvocationTable.invocationEnded.name()));
-			dataflowInvocation.setInvocationStarted(rs.getTimestamp(DataflowInvocationTable.invocationStarted.name()));
-			dataflowInvocation.setOutputsDataBindingId(rs.getString(DataflowInvocationTable.outputsDataBinding.name()));
-			dataflowInvocation.setParentProcessorEnactmentId(rs.getString(DataflowInvocationTable.parentProcessorEnactmentId.name()));
-			dataflowInvocation.setWorkflowId(rs.getString(DataflowInvocationTable.workflowId.name()));
-			dataflowInvocation.setWorkflowRunId(rs.getString(DataflowInvocationTable.workflowRunId.name()));
-			dataflowInvocation.setCompleted(rs.getBoolean(DataflowInvocationTable.completed.name()));
-			if (rs.next()) {
-				logger.error("Found more than one DataflowInvocation for workflowRunId=" + workflowRunId);
-				return null;
-			}
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query " + query, e);
-		}
-		return dataflowInvocation;
-	}
-
-	public DataflowInvocation getDataflowInvocation(
-			ProcessorEnactment processorEnactment) {
-		String query = "SELECT " + DataflowInvocationTable.dataflowInvocationId
-				+ "," + DataflowInvocationTable.inputsDataBinding + ","
-				+ DataflowInvocationTable.invocationEnded + ","
-				+ DataflowInvocationTable.invocationStarted + ","
-				+ DataflowInvocationTable.outputsDataBinding + ","
-				+ DataflowInvocationTable.parentProcessorEnactmentId + ","
-				+ DataflowInvocationTable.workflowId + ","
-				+ DataflowInvocationTable.workflowRunId + ","
-				+ DataflowInvocationTable.completed + " FROM "
-				+ DataflowInvocationTable.DataflowInvocation + " WHERE "
-				+ DataflowInvocationTable.parentProcessorEnactmentId + "=?";
-		DataflowInvocation dataflowInvocation = null;
-		try (Connection connection = getConnection();
-				PreparedStatement statement = connection
-						.prepareStatement(query)) {
-			statement.setString(1, processorEnactment.getProcessEnactmentId());
-			ResultSet rs = statement.executeQuery();
-			if (!rs.next()) {
-				logger.warn("Could not find DataflowInvocation for processorEnactmentId="
-						+ processorEnactment.getProcessEnactmentId());
-				return null;
-			}
-			dataflowInvocation = new DataflowInvocation();
-			dataflowInvocation.setDataflowInvocationId(rs
-					.getString(DataflowInvocationTable.dataflowInvocationId
-							.name()));
-			dataflowInvocation
-					.setInputsDataBindingId(rs
-							.getString(DataflowInvocationTable.inputsDataBinding
-									.name()));
-			dataflowInvocation.setInvocationEnded(rs
-					.getTimestamp(DataflowInvocationTable.invocationEnded
-							.name()));
-			dataflowInvocation.setInvocationStarted(rs
-					.getTimestamp(DataflowInvocationTable.invocationStarted
-							.name()));
-			dataflowInvocation.setOutputsDataBindingId(rs
-					.getString(DataflowInvocationTable.outputsDataBinding
-							.name()));
-			dataflowInvocation
-					.setParentProcessorEnactmentId(rs
-							.getString(DataflowInvocationTable.parentProcessorEnactmentId
-									.name()));
-			dataflowInvocation.setWorkflowId(rs
-					.getString(DataflowInvocationTable.workflowId.name()));
-			dataflowInvocation.setWorkflowRunId(rs
-					.getString(DataflowInvocationTable.workflowRunId.name()));
-			dataflowInvocation.setCompleted(rs
-					.getBoolean(DataflowInvocationTable.completed.name()));
-
-			if (rs.next()) {
-				logger.error("Found more than one DataflowInvocation for processorEnactmentId="
-						+ processorEnactment.getProcessEnactmentId());
-				return null;
-			}
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query " + query, e);
-		}
-		return dataflowInvocation;
-	}
-
-	public List<DataflowInvocation> getDataflowInvocations(String workflowRunId) {
-		String query = "SELECT " + DataflowInvocationTable.dataflowInvocationId
-				+ "," + DataflowInvocationTable.inputsDataBinding + ","
-				+ DataflowInvocationTable.invocationEnded + ","
-				+ DataflowInvocationTable.invocationStarted + ","
-				+ DataflowInvocationTable.outputsDataBinding + ","
-				+ DataflowInvocationTable.parentProcessorEnactmentId + ","
-				+ DataflowInvocationTable.workflowId + ","
-				+ DataflowInvocationTable.workflowRunId + ","
-				+ DataflowInvocationTable.completed + " FROM "
-				+ DataflowInvocationTable.DataflowInvocation + " WHERE "
-				+ DataflowInvocationTable.workflowRunId + "=?";
-		List<DataflowInvocation> invocations = new ArrayList<>();
-		try (Connection connection = getConnection();
-				PreparedStatement statement = connection
-						.prepareStatement(query)) {
-			statement.setString(1, workflowRunId);
-			ResultSet rs = statement.executeQuery();
-			if (! rs.next()) {
-				logger.warn("Could not find DataflowInvocation for workflowRunId=" + workflowRunId);
-				return null;
-			}
-			DataflowInvocation dataflowInvocation = new DataflowInvocation();
-			dataflowInvocation.setDataflowInvocationId(rs.getString(DataflowInvocationTable.dataflowInvocationId.name()));
-			dataflowInvocation.setInputsDataBindingId(rs.getString(DataflowInvocationTable.inputsDataBinding.name()));
-			dataflowInvocation.setInvocationEnded(rs.getTimestamp(DataflowInvocationTable.invocationEnded.name()));
-			dataflowInvocation.setInvocationStarted(rs.getTimestamp(DataflowInvocationTable.invocationStarted.name()));
-			dataflowInvocation.setOutputsDataBindingId(rs.getString(DataflowInvocationTable.outputsDataBinding.name()));
-			dataflowInvocation.setParentProcessorEnactmentId(rs.getString(DataflowInvocationTable.parentProcessorEnactmentId.name()));
-			dataflowInvocation.setWorkflowId(rs.getString(DataflowInvocationTable.workflowId.name()));
-			dataflowInvocation.setWorkflowRunId(rs.getString(DataflowInvocationTable.workflowRunId.name()));
-			dataflowInvocation.setCompleted(rs.getBoolean(DataflowInvocationTable.completed.name()));
-			invocations.add(dataflowInvocation);
-		} catch (SQLException | InstantiationException | IllegalAccessException | ClassNotFoundException e) {
-			logger.warn("Could not execute query " + query, e);
-		}
-		return invocations;
-	}
-
-	public List<Collection> getCollectionsForRun(String wfInstanceID) {
-		ArrayList<Collection> result = new ArrayList<>();
-		String sql = "SELECT * FROM Collection C WHERE workflowRunId = ?";
-		try (Connection c = getConnection();
-				PreparedStatement ps = c.prepareStatement(sql)) {
-			ps.setString(1, wfInstanceID);
-			ResultSet rs = ps.executeQuery();
-			while (rs.next()) {
-				Collection coll = new Collection();
-				coll.setCollId(rs.getString(CollectionTable.collID.name()));
-				coll.setParentIdentifier(rs
-						.getString(CollectionTable.parentCollIDRef.name()));
-				coll.setWorkflowRunIdentifier(rs
-						.getString(CollectionTable.workflowRunId.name()));
-				coll.setProcessorName(rs
-						.getString(CollectionTable.processorNameRef.name()));
-				coll.setPortName(rs.getString(CollectionTable.portName.name()));
-				coll.setIteration(rs.getString(CollectionTable.iteration.name()));
-				result.add(coll);
-			}
-		} catch (Exception e) {
-			logger.warn("Could not execute query", e);
-		}
-		return result;
-	}
-}