You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:43:15 UTC
[11/51] [partial] incubator-taverna-engine git commit: temporarily
empty repository
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/Port.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Port.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Port.java
deleted file mode 100644
index 4c2af25..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Port.java
+++ /dev/null
@@ -1,198 +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;
-
-/**
- * a Port that has no pName is either a WF input or output, depending on isInput
- *
- * @author Paolo Missier
- */
-public class Port {
-
- @Override
- public String toString() {
- return "Port [identifier=" + identifier + ", isInputPort="
- + isInputPort + ", portName=" + portName + ", processorName="
- + processorName + ", workflowId=" + workflowId + "]";
- }
-
- @Override
- public int hashCode() {
- return 31 + ((identifier == null) ? 0 : identifier.hashCode());
- }
-
- @Override
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- Port other = (Port) obj;
- if (identifier == null) {
- if (other.identifier != null)
- return false;
- } else if (!identifier.equals(other.identifier))
- return false;
- return true;
- }
-
- private String identifier;
- private String portName;
- private String processorName;
- private boolean isInputPort;
- private String workflowId;
- private int depth = 0;
- private Integer resolvedDepth = null;
- private int iterationStrategyOrder = 0;
- private String processorId;
-
- /**
- * @return the workflowId
- */
- public String getWorkflowId() {
- return workflowId;
- }
-
- /**
- * @param workflowId
- * the workflowId to set
- */
- public void setWorkflowId(String workflowId) {
- this.workflowId = workflowId;
- }
-
- /**
- * @return the vName
- */
- public String getPortName() {
- return portName;
- }
-
- /**
- * @param name
- * the portName to set
- */
- public void setPortName(String portName) {
- this.portName = portName;
- }
-
- /**
- * @return the processorName
- */
- public String getProcessorName() {
- return processorName;
- }
-
- /**
- * @param name
- * the processorName to set
- */
- public void setProcessorName(String processorName) {
- this.processorName = processorName;
- }
-
- /**
- * @return <code>true</code> if the port is an input port,
- * <code>false</code> if it is an output port
- */
- public boolean isInputPort() {
- return isInputPort;
- }
-
- /**
- * @param isInputPort
- * <code>true</code> if the port is an input port,
- * <code>false</code> if it is an output port
- */
- public void setInputPort(boolean isInputPort) {
- this.isInputPort = isInputPort;
- }
-
- /**
- * @return the depth
- */
- public int getDepth() {
- return depth;
- }
-
- /**
- * @param depth
- * the depth to set
- */
- public void setDepth(int depth) {
- this.depth = depth;
- }
-
- /**
- * @return the resolvedDepth
- */
- public Integer getResolvedDepth() {
- return resolvedDepth;
- }
-
- /**
- * @param resolvedDepth
- * the resolvedDepth to set
- */
- public void setResolvedDepth(Integer resolvedDepth) {
- this.resolvedDepth = resolvedDepth;
- }
-
- /**
- * @return <code>true</code> if the {@link #resolvedDepth} has been set
- */
- public boolean isResolvedDepthSet() {
- return resolvedDepth != null;
- }
-
- public void setIdentifier(String identifier) {
- this.identifier = identifier;
- }
-
- public String getIdentifier() {
- return identifier;
- }
-
- /**
- * @return the iterationStrategyOrder
- */
- public int getIterationStrategyOrder() {
- return iterationStrategyOrder;
- }
-
- /**
- * @param iterationStrategyOrder
- * the iterationStrategyOrder to set
- */
- public void setIterationStrategyOrder(int iterationStrategyOrder) {
- this.iterationStrategyOrder = iterationStrategyOrder;
- }
-
- public String getProcessorId() {
- return processorId;
- }
-
- public void setProcessorId(String processorId) {
- this.processorId = processorId;
- }
-}
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/PortBinding.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/PortBinding.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/PortBinding.java
deleted file mode 100644
index c6b0b86..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/PortBinding.java
+++ /dev/null
@@ -1,258 +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 Missier
- *
- */
-public class PortBinding {
- private String workflowId;
- private String portName;
- private String workflowRunId;
- private String value;
- private String collIDRef;
- private int positionInColl;
- private String processorName;
- private String valueType;
- private String reference;
- private String iteration;
- private String resolvedValue;
- private String portId;
- private Boolean isInputPort;
-
- public PortBinding() {
- }
-
- public PortBinding(PortBinding vb) {
- workflowId = vb.workflowId;
- portName = vb.portName;
- workflowRunId = vb.workflowRunId;
- value = vb.value;
- collIDRef = vb.collIDRef;
- positionInColl = vb.positionInColl;
- processorName = vb.processorName;
- valueType = vb.valueType;
- reference = vb.reference;
- iteration = vb.iteration;
- resolvedValue = vb.resolvedValue;
- portId = vb.portId;
- isInputPort = vb.isInputPort;
- }
-
- public String getPortId() {
- return portId;
- }
-
- @Override
- public String toString() {
- return "PortBinding [workflowId=" + workflowId + ", portName="
- + portName + ", workflowRunId=" + workflowRunId + ", value="
- + value + ", collIDRef=" + collIDRef + ", positionInColl="
- + positionInColl + ", processorName=" + processorName
- + ", valueType=" + valueType + ", reference=" + reference
- + ", iteration=" + iteration + ", resolvedValue="
- + resolvedValue + ", portId=" + portId + ", isInputPort="
- + isInputPort + "]";
- }
-
- /**
- * @return the positionInColl
- */
- public int getPositionInColl() {
- return positionInColl;
- }
-
- /**
- * @param positionInColl
- * the positionInColl to set
- */
- public void setPositionInColl(int positionInColl) {
- this.positionInColl = positionInColl;
- }
-
- /**
- * @return the valueType
- */
- public String getValueType() {
- return valueType;
- }
-
- /**
- * @param valueType
- * the valueType to set
- */
- public void setValueType(String valueType) {
- this.valueType = valueType;
- }
-
- /**
- * @return the portName
- */
- public String getPortName() {
- return portName;
- }
-
- /**
- * @param portName
- * the portName to set
- */
- public void setPortName(String portName) {
- this.portName = portName;
- }
-
- /**
- * @return the workflowRunId
- */
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- /**
- * @param workflowRunId
- * the workflowRunId to set
- */
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-
- /**
- * @return the processorName
- */
- public String getProcessorName() {
- return processorName;
- }
-
- /**
- * @param processorName
- * the processorName to set
- */
- public void setProcessorName(String processorName) {
- this.processorName = processorName;
- }
-
- /**
- * @return the collIDRef
- */
- public String getCollIDRef() {
- return collIDRef;
- }
-
- /**
- * @param collIDRef
- * the collIDRef to set
- */
- public void setCollIDRef(String collIDRef) {
- this.collIDRef = collIDRef;
- }
-
- /**
- * @return the iteration
- */
- public String getIteration() {
- return iteration;
- }
-
- /**
- * @param iterationVector
- * the iteration to set
- */
- public void setIteration(String iterationVector) {
- this.iteration = iterationVector;
- }
-
- /**
- * @return the value
- */
- public String getValue() {
- return value;
- }
-
- /**
- * @param value
- * the value to set
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * @return the ref
- */
- public String getReference() {
- return reference;
- }
-
- /**
- * @param ref
- * the ref to set
- */
- public void setReference(String ref) {
- this.reference = ref;
- }
-
- /**
- * @return the resolvedValue
- */
- public String getResolvedValue() {
- return resolvedValue;
- }
-
- /**
- * @param resolvedValue
- * the resolvedValue to set
- */
- public void setResolvedValue(String resolvedValue) {
- this.resolvedValue = resolvedValue;
- }
-
- /**
- * @return the workflowId
- */
- public String getWorkflowId() {
- return workflowId;
- }
-
- /**
- * @param workflowId
- * the workflowId to set
- */
- public void setWorkflowId(String workflowId) {
- this.workflowId = workflowId;
- }
-
- public void setPortId(String portId) {
- this.portId = portId;
-
- }
-
- public void setIsInputPort(boolean isInputPort) {
- this.setInputPort(isInputPort);
- }
-
- public void setInputPort(boolean isInputPort) {
- this.isInputPort = isInputPort;
- }
-
- public Boolean isInputPort() {
- return isInputPort;
- }
-}
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/ProcessorBinding.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProcessorBinding.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProcessorBinding.java
deleted file mode 100644
index 46a8565..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProcessorBinding.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 Missier
- *
- */
-public class ProcessorBinding {
- private String identifier;
-
- private String processorName;
- private String workflowRunId;
- private String workflowId;
- private String firstActivityClassName;
- private String iterationVector;
-
- @Override
- public String toString() {
- return "ProcessorBinding [firstActivityClassName="
- + firstActivityClassName + ", identifier=" + identifier
- + ", iterationVector=" + iterationVector + ", processorName="
- + processorName + ", workflowId=" + workflowId
- + ", workflowRunId=" + workflowRunId + "]";
- }
-
- /**
- * @return the processorNameRef
- */
- public String getProcessorName() {
- return processorName;
- }
-
- /**
- * @param nameRef
- * the processorNameRef to set
- */
- public void setProcessorName(String processorNameRef) {
- this.processorName = processorNameRef;
- }
-
- /**
- * @return the execIDRef
- */
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- /**
- * @param workflowRunId
- * the workflowRunId to set
- */
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-
- /**
- * @return the actName
- */
- public String getFirstActivityClassName() {
- return firstActivityClassName;
- }
-
- /**
- * @param actName
- * the actName to set
- */
- public void setFirstActivityClassName(String actName) {
- this.firstActivityClassName = actName;
- }
-
- /**
- * @return the iteration
- */
- public String getIterationVector() {
- return iterationVector;
- }
-
- /**
- * @param iterationVector
- * the iteration to set
- */
- public void setIterationVector(String iterationVector) {
- this.iterationVector = iterationVector;
- }
-
- public void setIdentifier(String identifier) {
- this.identifier = identifier;
- }
-
- public String getIdentifier() {
- return identifier;
- }
-
- /**
- * @return the workflowId
- */
- public String getWorkflowId() {
- return workflowId;
- }
-
- /**
- * @param workflowId
- * the workflowId to set
- */
- public void setWorkflowId(String workflowId) {
- this.workflowId = workflowId;
- }
-}
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/ProcessorEnactment.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProcessorEnactment.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProcessorEnactment.java
deleted file mode 100644
index fd59fdf..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProcessorEnactment.java
+++ /dev/null
@@ -1,151 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-import java.sql.Timestamp;
-
-public class ProcessorEnactment {
- private Timestamp enactmentEnded;
- private Timestamp enactmentStarted;
- private String finalOutputsDataBindingId;
- private String initialInputsDataBindingId;
- private String iteration;
- private String parentProcessorEnactmentId;
- private String processEnactmentId;
- private String processIdentifier;
- private String processorId;
- private String workflowRunId;
-
- @Override
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- ProcessorEnactment other = (ProcessorEnactment) obj;
- if (processEnactmentId == null) {
- if (other.processEnactmentId != null)
- return false;
- } else if (!processEnactmentId.equals(other.processEnactmentId))
- return false;
- return true;
- }
-
- public Timestamp getEnactmentEnded() {
- return enactmentEnded;
- }
-
- public Timestamp getEnactmentStarted() {
- return enactmentStarted;
- }
-
- public String getFinalOutputsDataBindingId() {
- return finalOutputsDataBindingId;
- }
-
- public String getInitialInputsDataBindingId() {
- return initialInputsDataBindingId;
- }
-
- public String getIteration() {
- return iteration;
- }
-
- public String getParentProcessorEnactmentId() {
- return parentProcessorEnactmentId;
- }
-
- public String getProcessEnactmentId() {
- return processEnactmentId;
- }
-
- public String getProcessIdentifier() {
- return processIdentifier;
- }
-
- public String getProcessorId() {
- return processorId;
- }
-
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- @Override
- public int hashCode() {
- final int prime = 31;
- int result = 1;
- result = prime
- * result
- + ((processEnactmentId == null) ? 0 : processEnactmentId
- .hashCode());
- return result;
- }
-
- public void setEnactmentEnded(Timestamp enactmentEnded) {
- this.enactmentEnded = enactmentEnded;
- }
-
- public void setEnactmentStarted(Timestamp enactmentStarted) {
- this.enactmentStarted = enactmentStarted;
- }
-
- public void setFinalOutputsDataBindingId(String finalOutputsDataBindingId) {
- this.finalOutputsDataBindingId = finalOutputsDataBindingId;
- }
-
- public void setInitialInputsDataBindingId(String initialInputsDataBindingId) {
- this.initialInputsDataBindingId = initialInputsDataBindingId;
- }
-
- public void setIteration(String iteration) {
- this.iteration = iteration;
- }
-
- public void setParentProcessorEnactmentId(String parentProcessorEnactmentId) {
- this.parentProcessorEnactmentId = parentProcessorEnactmentId;
- }
-
- public void setProcessEnactmentId(String processEnactmentId) {
- this.processEnactmentId = processEnactmentId;
- }
-
- public void setProcessIdentifier(String processIdentifier) {
- this.processIdentifier = processIdentifier;
- }
-
- public void setProcessorId(String processorId) {
- this.processorId = processorId;
- }
-
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("ProcessorEnactment [enactmentEnded=");
- builder.append(enactmentEnded);
- builder.append(", enactmentStarted=");
- builder.append(enactmentStarted);
- builder.append(", finalOutputs=");
- builder.append(finalOutputsDataBindingId);
- builder.append(", initialInputs=");
- builder.append(initialInputsDataBindingId);
- builder.append(", iteration=");
- builder.append(iteration);
- builder.append(", parentProcessEnactmentId=");
- builder.append(parentProcessorEnactmentId);
- builder.append(", processEnactmentId=");
- builder.append(processEnactmentId);
- builder.append(", processIdentifier=");
- builder.append(processIdentifier);
- builder.append(", processorId=");
- builder.append(processorId);
- builder.append(", workflowRunId=");
- builder.append(workflowRunId);
- builder.append("]");
- return builder.toString();
- }
-}
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/ProvenanceProcessor.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProvenanceProcessor.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProvenanceProcessor.java
deleted file mode 100644
index fb1a8fb..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProvenanceProcessor.java
+++ /dev/null
@@ -1,115 +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;
-
-/**
- * a Port that has no pName is either a WF input or output, depending on isInput
- *
- * @author Paolo Missier
- */
-public class ProvenanceProcessor {
-
- public static final String DATAFLOW_ACTIVITY = "net.sf.taverna.t2.activities.dataflow.DataflowActivity";
-
- private String identifier;
- private String processorName;
- private String workflowId;
- private String firstActivityClassName;
- private boolean isTopLevelProcessor;
-
- public ProvenanceProcessor() {
- }
-
- @Override
- public String toString() {
- StringBuilder sb = new StringBuilder();
- sb.append("PROCESSOR: ****").append("\nworkflow: " + getWorkflowId())
- .append("\nprocessor name: " + getProcessorName())
- .append("\ntype: " + getFirstActivityClassName());
-
- return sb.toString();
- }
-
- /**
- * @return the workflowId
- */
- public String getWorkflowId() {
- return workflowId;
- }
-
- /**
- * @param workflowId
- * the workflowId to set
- */
- public void setWorkflowId(String workflowId) {
- this.workflowId = workflowId;
- }
-
- /**
- * @return The fully qualified classname for the first activity in this
- * processor, or {@link #DATAFLOW_ACTIVITY} if this is a virtual
- * processor representing the workflow itself.
- */
- public String getFirstActivityClassName() {
- return firstActivityClassName;
- }
-
- /**
- * @param firstActivityClassName
- * The fully qualified classname for the first activity in this
- * processor, or {@link #DATAFLOW_ACTIVITY} if this is a virtual
- * processor representing the workflow itself.
- */
- public void setFirstActivityClassName(String firstActivityClassName) {
- this.firstActivityClassName = firstActivityClassName;
- }
-
- /**
- * @return the processorName
- */
- public String getProcessorName() {
- return processorName;
- }
-
- /**
- * @param processorName
- * the processorName to set
- */
- public void setProcessorName(String processorName) {
- this.processorName = processorName;
- }
-
- public void setIdentifier(String identifier) {
- this.identifier = identifier;
- }
-
- public String getIdentifier() {
- return identifier;
- }
-
- public void setTopLevelProcessor(boolean isTopLevelProcessor) {
- this.isTopLevelProcessor = isTopLevelProcessor;
- }
-
- public boolean isTopLevelProcessor() {
- return isTopLevelProcessor;
- }
-}
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/ProvenanceUtils.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProvenanceUtils.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProvenanceUtils.java
deleted file mode 100644
index a36308a..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ProvenanceUtils.java
+++ /dev/null
@@ -1,128 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-import static net.sf.taverna.t2.provenance.vocabulary.SharedVocabulary.INPUTDATA_EVENT_TYPE;
-
-import java.util.Set;
-import java.util.regex.Pattern;
-
-import net.sf.taverna.t2.provenance.item.DataProvenanceItem;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.IdentifiedList;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceSet;
-import net.sf.taverna.t2.reference.T2Reference;
-
-import org.jdom.Element;
-import org.tupeloproject.kernel.NotFoundException;
-
-public class ProvenanceUtils {
- public static Pattern parentProcessPattern = Pattern.compile("^(.*):?[^:]+:[^:]+$");
-
- public static String iterationToString(int[] iteration) {
- String result = "[";
- for (int i = 0; i < iteration.length; i++) {
- result += iteration[i];
- if (i < (iteration.length - 1))
- result += ",";
- }
- result += "]";
- return result;
- }
-
- /**
- * Returns an Element representing the data item, identfied as either input
- * or output. References to data are currently resolved to their actual
- * values
- */
- public static Element getDataItemAsXML(DataProvenanceItem provenanceItem) {
- String name;
- if (provenanceItem.getEventType().equals(INPUTDATA_EVENT_TYPE)) {
- name = "inputdata";
- } else {
- name = "outputdata";
- }
- Element result = new Element(name);
- result.setAttribute("identifier", provenanceItem.getIdentifier());
- result.setAttribute("processID", provenanceItem.getProcessId());
- result.setAttribute("parent", provenanceItem.getParentId());
- for (String port : provenanceItem.getDataMap().keySet()) {
- Element portElement = new Element("port");
- portElement.setAttribute("name", port);
- portElement.setAttribute(
- "depth",
- Integer.toString(provenanceItem.getDataMap().get(port)
- .getDepth()));
- result.addContent(portElement);
- portElement.addContent(resolveToElement(provenanceItem.getDataMap()
- .get(port), provenanceItem.getReferenceService()));
- Element element = new Element("some_stuff");
- portElement.addContent(element);
- }
- return result;
- }
-
- /**
- * Given a {@link T2Reference} return all the other {@link T2Reference}s
- * which it contains as an XML Element.
- *
- * @param entityIdentifier
- * @return
- * @throws NotFoundException
- * @throws RetrievalException
- */
- private static org.jdom.Element resolveToElement(T2Reference reference,
- ReferenceService referenceService) {
- Element element = new Element("resolvedReference");
- switch (reference.getReferenceType()) {
- case ErrorDocument:
- ErrorDocument error = referenceService.getErrorDocumentService()
- .getError(reference);
-
- element.setName("error");
- element.setAttribute("id", reference.toString());
- Element messageElement = new Element("message");
- messageElement.addContent(error.getExceptionMessage());
- element.addContent(messageElement);
- break;
- case ReferenceSet:
- element.setName("referenceSet");
- element.setAttribute("id", reference.toString());
- ReferenceSet referenceSet = referenceService
- .getReferenceSetService().getReferenceSet(reference);
- Set<ExternalReferenceSPI> externalReferences = referenceSet
- .getExternalReferences();
- for (ExternalReferenceSPI externalReference : externalReferences) {
- // FIXME does this make sense? No!! Should get the actual value
- // not what it is (TEXT etc)
- Element refElement = new Element("reference");
- refElement.addContent(externalReference.getDataNature()
- .toString());
- element.addContent(refElement);
- }
- break;
- case IdentifiedList:
- IdentifiedList<T2Reference> list = referenceService
- .getListService().getList(reference);
-
- element.setName("list");
- element.setAttribute("id", reference.toString());
- for (T2Reference ref : list)
- element.addContent(resolveToElement(ref, referenceService));
- break;
- default:
- // throw something (maybe a tantrum)
- }
- return element;
- }
-
- public static String parentProcess(String processId, int levels) {
- if (levels < 1)
- return processId;
- int lastColon = processId.lastIndexOf(":");
- if (lastColon == -1)
- return null;
- return parentProcess(processId.substring(0, lastColon), --levels);
- }
-
-}
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/QueryPort.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/QueryPort.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/QueryPort.java
deleted file mode 100644
index 34b4f9b..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/QueryPort.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-/**
- * @author Paolo Missier
- * <p/>
- *
- */
-public class QueryPort {
- private String workflowRunId;
- private String workflowId;
- private String processorName;
- private String portName;
- private String path;
- private String value;
-
- @Override
- public String toString() {
- StringBuilder sb = new StringBuilder();
- sb.append("PORT: ****").append("\nworkflow: " + getWorkflowId())
- .append("\nprocessor: " + getProcessorName())
- .append("\nport: " + getPortName())
- .append("\npath to value: " + getPath());
-
- return sb.toString();
- }
-
- /**
- * @return the processorName
- */
- public String getProcessorName() {
- return processorName;
- }
-
- /**
- * @param processorName
- * the processorName to set
- */
- public void setProcessorName(String processorName) {
- this.processorName = processorName;
- }
-
- /**
- * @return the vname
- */
- public String getPortName() {
- return portName;
- }
-
- /**
- * @param vname
- * the vname to set
- */
- public void setPortName(String vname) {
- this.portName = vname;
- }
-
- /**
- * @return the path
- */
- public String getPath() {
- return path;
- }
-
- /**
- * @param path
- * the path to set
- */
- public void setPath(String path) {
- this.path = path;
- }
-
- /**
- * @return the value
- */
- public String getValue() {
- return value;
- }
-
- /**
- * @param value
- * the value to set
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * @return the workflowRunId
- */
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- /**
- * @param workflowRunId
- * the workflowRunId to set
- */
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-
- /**
- * @return the workflowId
- */
- public String getWorkflowId() {
- return workflowId;
- }
-
- /**
- * @param workflowId
- * the workflowId to set
- */
- public void setWorkflowId(String workflowId) {
- this.workflowId = workflowId;
- }
-}
\ No newline at end of file
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/ServiceInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ServiceInvocation.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ServiceInvocation.java
deleted file mode 100644
index 83de7ce..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/ServiceInvocation.java
+++ /dev/null
@@ -1,161 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-import java.sql.Timestamp;
-
-public class ServiceInvocation {
- private ProcessorEnactment processorEnactment;
- private String workflowRunId;
- private long invocationNumber;
- private Timestamp invocationStarted;
- private Timestamp invocationEnded;
- private DataBinding inputs;
- private DataBinding outputs;
- private String failureT2Reference;
- private Activity activity;
- private String initiatingDispatchLayer;
- private String finalDispatchLayer;
-
- public ProcessorEnactment getProcessorEnactment() {
- return processorEnactment;
- }
-
- public void setProcessorEnactment(ProcessorEnactment processorEnactment) {
- this.processorEnactment = processorEnactment;
- }
-
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-
- public long getInvocationNumber() {
- return invocationNumber;
- }
-
- public void setInvocationNumber(long invocationNumber) {
- this.invocationNumber = invocationNumber;
- }
-
- public Timestamp getInvocationStarted() {
- return invocationStarted;
- }
-
- public void setInvocationStarted(Timestamp invocationStarted) {
- this.invocationStarted = invocationStarted;
- }
-
- public Timestamp getInvocationEnded() {
- return invocationEnded;
- }
-
- public void setInvocationEnded(Timestamp invocationEnded) {
- this.invocationEnded = invocationEnded;
- }
-
- public DataBinding getInputs() {
- return inputs;
- }
-
- public void setInputs(DataBinding inputs) {
- this.inputs = inputs;
- }
-
- public DataBinding getOutputs() {
- return outputs;
- }
-
- public void setOutputs(DataBinding outputs) {
- this.outputs = outputs;
- }
-
- public String getFailureT2Reference() {
- return failureT2Reference;
- }
-
- public void setFailureT2Reference(String failureT2Reference) {
- this.failureT2Reference = failureT2Reference;
- }
-
- public Activity getActivity() {
- return activity;
- }
-
- public void setActivity(Activity activity) {
- this.activity = activity;
- }
-
- public String getInitiatingDispatchLayer() {
- return initiatingDispatchLayer;
- }
-
- public void setInitiatingDispatchLayer(String initiatingDispatchLayer) {
- this.initiatingDispatchLayer = initiatingDispatchLayer;
- }
-
- public String getFinalDispatchLayer() {
- return finalDispatchLayer;
- }
-
- public void setFinalDispatchLayer(String finalDispatchLayer) {
- this.finalDispatchLayer = finalDispatchLayer;
- }
-
- @Override
- public int hashCode() {
- return 31
- * (int) (invocationNumber ^ (invocationNumber >>> 32))
- + ((processorEnactment == null) ? 0 : processorEnactment
- .hashCode());
- }
-
- @Override
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- ServiceInvocation other = (ServiceInvocation) obj;
- if (invocationNumber != other.invocationNumber)
- return false;
- if (processorEnactment == null) {
- if (other.processorEnactment != null)
- return false;
- } else if (!processorEnactment.equals(other.processorEnactment))
- return false;
- return true;
- }
-
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("ServiceInvocation [activity=");
- builder.append(activity);
- builder.append(", failureT2Reference=");
- builder.append(failureT2Reference);
- builder.append(", finalDispatchLayer=");
- builder.append(finalDispatchLayer);
- builder.append(", initiatingDispatchLayer=");
- builder.append(initiatingDispatchLayer);
- builder.append(", inputs=");
- builder.append(inputs);
- builder.append(", invocationEnded=");
- builder.append(invocationEnded);
- builder.append(", invocationNumber=");
- builder.append(invocationNumber);
- builder.append(", invocationStarted=");
- builder.append(invocationStarted);
- builder.append(", outputs=");
- builder.append(outputs);
- builder.append(", processorEnactment=");
- builder.append(processorEnactment);
- builder.append(", workflowRunId=");
- builder.append(workflowRunId);
- builder.append("]");
- return builder.toString();
- }
-}
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/Workflow.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Workflow.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Workflow.java
deleted file mode 100644
index b1f75ef..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/Workflow.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-public class Workflow {
- private String workflowId;
- private String parentWorkflowId;
- private String externalName;
-
- public void setWorkflowId(String workflowId) {
- this.workflowId = workflowId;
- }
-
- public String getWorkflowId() {
- return workflowId;
- }
-
- public void setParentWorkflowId(String parentIdentifier) {
- this.parentWorkflowId = parentIdentifier;
- }
-
- public String getParentWorkflowId() {
- return parentWorkflowId;
- }
-
- /**
- * @return the externalName
- */
- public String getExternalName() {
- return externalName;
- }
-
- /**
- * @param externalName the externalName to set
- */
- public void setExternalName(String externalName) {
- this.externalName = externalName;
- }
-}
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/WorkflowRun.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/WorkflowRun.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/WorkflowRun.java
deleted file mode 100644
index 8e5b25a..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/WorkflowRun.java
+++ /dev/null
@@ -1,72 +0,0 @@
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-import java.sql.Blob;
-
-public class WorkflowRun {
- private String workflowRunId;
- /**
- * this is the workflowId for the TOP LEVEL workflow for this run.
- * <p>
- * CHECK
- */
- private String workflowId;
- private String timestamp;
- private String workflowExternalName;
- private byte[] dataflowBlob;
-
- public void setWorkflowId(String workflowIdentifier) {
- this.workflowId = workflowIdentifier;
- }
-
- public String getWorkflowId() {
- return workflowId;
- }
-
- public void setTimestamp(String timestamp) {
- this.timestamp = timestamp;
- }
-
- public String getTimestamp() {
- return timestamp;
- }
-
- /**
- * @return the workflowRunId
- */
- public String getWorkflowRunId() {
- return workflowRunId;
- }
-
- /**
- * @param workflowRunId the workflowRunId to set
- */
- public void setWorkflowRunId(String workflowRunId) {
- this.workflowRunId = workflowRunId;
- }
-
- /**
- * @return the workflowExternalName
- */
- public String getWorkflowExternalName() {
- return workflowExternalName;
- }
-
- /**
- * @param workflowExternalName the workflowExternalName to set
- */
- public void setWorkflowExternalName(String workflowExternalName) {
- this.workflowExternalName = workflowExternalName;
- }
-
- /**
- * A {@link Blob} object representing the dataflow
- * @param bs
- */
- public void setDataflowBlob(byte[] bs) {
- this.dataflowBlob = bs;
- }
-
- public byte[] getDataflowBlob() {
- return dataflowBlob;
- }
-}
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/WorkflowTree.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/WorkflowTree.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/WorkflowTree.java
deleted file mode 100644
index 7db0259..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/utils/WorkflowTree.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.provenance.lineageservice.utils;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * a tree structure used to describe the nested static structure of a workflow
- * as it is found in the provenance DB
- *
- * @author Paolo Missier
- */
-public class WorkflowTree {
- private Workflow node;
- private List<WorkflowTree> children = new ArrayList<>();
-
- /**
- * @return the children
- */
- public List<WorkflowTree> getChildren() {
- return children;
- }
-
- /**
- * @param children
- * the children to set
- */
- public void setChildren(List<WorkflowTree> children) {
- this.children = children;
- }
-
- /**
- * @return the node
- */
- public Workflow getNode() {
- return node;
- }
-
- /**
- * @param node
- * the node to set
- */
- public void setNode(Workflow node) {
- this.node = node;
- }
-
- public void addChild(WorkflowTree childStructure) {
- children.add(childStructure);
- }
-
- @Override
- public String toString() {
- return toString(new StringBuilder(), 0);
- }
-
- public String toString(int indent) {
- return toString(new StringBuilder(), indent);
- }
-
- protected String toString(StringBuilder sb, int indent) {
- sb.append(getNode().getExternalName() + "\n");
- for (WorkflowTree tree : getChildren()) {
- indent++;
- for (int i = 1; i < indent; i++)
- sb.append("-");
- sb.append(tree.toString(indent));
- indent--;
- }
- return sb.toString();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/opm/OPMImporter.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/opm/OPMImporter.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/opm/OPMImporter.java
deleted file mode 100644
index f491683..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/opm/OPMImporter.java
+++ /dev/null
@@ -1,541 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.provenance.opm;
-
-import java.io.File;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
-
-import net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter;
-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 org.openprovenance.model.Account;
-import org.openprovenance.model.AccountRef;
-import org.openprovenance.model.Accounts;
-import org.openprovenance.model.Artifact;
-import org.openprovenance.model.ArtifactRef;
-import org.openprovenance.model.Artifacts;
-import org.openprovenance.model.Dependencies;
-import org.openprovenance.model.OPMDeserialiser;
-import org.openprovenance.model.OPMGraph;
-import org.openprovenance.model.Process;
-import org.openprovenance.model.ProcessRef;
-import org.openprovenance.model.Role;
-import org.openprovenance.model.Used;
-import org.openprovenance.model.WasControlledBy;
-import org.openprovenance.model.WasDerivedFrom;
-import org.openprovenance.model.WasGeneratedBy;
-import org.openprovenance.model.WasTriggeredBy;
-
-/**
- * imports foreign XML-serialized OPM graphs into the native Taverna provenance
- * DB, so they can be queried using
- * {@link net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis}
- *
- * @author paolo
- */
-public class OPMImporter {
- private static final String PROC_NAME = "P";
- private static final String OPM_DEF_ACCOUNT = "OPMDefaultAccount";
- private static Logger logger = Logger.getLogger(OPMImporter.class);
-
- private ProvenanceWriter pw;
- private OPMGraph graph;
-
- // Maps Account names to Taverna workflows
- private Map<String, String> accountToWorkflow = new HashMap<>();
- private Map<String, String> workflowToInstance = new HashMap<>();
-
- // maps workflowId --> (workflowId --> List(Port))
- private Map<String, Map<String, List<Port>>> usedVarsByAccount = new HashMap<>();
- private Map<String, Map<String, List<Port>>> wgbVarsByAccount = new HashMap<>();
-
- // maps accountname --> (artifact -> List(Process))
- private Map<String, Map<String, List<String>>> wgbArtifactsByAccount = new HashMap<>();
-
- // maps accountname --> (artifact -> List(Process))
- private Map<String, Map<String, List<String>>> usedArtifactsByAccount = new HashMap<>();
-
- private int procNameCounter;
-
- public OPMImporter(ProvenanceWriter pw) {
- this.pw = pw;
- }
-
- /**
- * orphan artifacts are those that are in the graph but are never used
- * neither generated. this indicates some problem with the graph structure.
- * this method is used for diagnostics after import has finished
- *
- * @return
- */
- public List<String> getOrphanArtifacts() {
- List<String> allwgb = new ArrayList<>();
- List<String> allUsed = new ArrayList<>();
- List<String> orphans = new ArrayList<>();
-
- if (graph == null) {
- logger.warn("null graph while attempting to count orphan artifacts -- giving up");
- return orphans;
- }
-
- Artifacts allArtifacts = graph.getArtifacts();
-
- for (Map.Entry<String, Map<String, List<String>>> entry : wgbArtifactsByAccount
- .entrySet())
- allwgb.addAll(entry.getValue().keySet());
- for (Map.Entry<String, Map<String, List<String>>> entry : usedArtifactsByAccount
- .entrySet())
- allUsed.addAll(entry.getValue().keySet());
-
- for (Artifact a : allArtifacts.getArtifact())
- if (!allwgb.contains(a.getId()) && !allUsed.contains(a.getId()))
- orphans.add(a.getId());
- return orphans;
- }
-
- public void importGraph(String XMLOPMGraphFilename) throws Exception,
- SQLException {
- try {
- logger.info("Importing OPM XML from file " + XMLOPMGraphFilename);
-
- // deserialize an XML OPM graph from file
- OPMDeserialiser deser = new OPMDeserialiser();
- graph = deser.deserialiseOPMGraph(new File(XMLOPMGraphFilename));
-
- } catch (Exception e) {
- logger.fatal("exception while deserializing -- unable to continue");
- logger.fatal(e.getMessage());
- return;
- }
-
- logger.debug("XML graph deserialized");
-
- /*
- * generates one pair <workflowId, workflowRun> for each account in the
- * graph
- */
- try {
- Accounts accounts = graph.getAccounts();
-
- // use this global account alongside any other that may be defined in the graph
- generateWFFromAccount(OPM_DEF_ACCOUNT);
-
- if (accounts == null) {
- logger.warn("this graph contains no accounts -- using only the default");
- } else {
- for (Account acc:accounts.getAccount())
- // writes both workflow and instance into the DB, updates accountToWorkflow
- generateWFFromAccount(acc.getId());
- }
- } catch (Exception e) {
- logger.warn("exception while getting accounts for this graph");
- }
-
- // what have we got?
- // retrieve all OPM relations from the graph
- Dependencies dependencies = graph.getDependencies();
-
- /*
- * associates processes and ports to workflows and varbindings to
- * corresponding workflowRuns
- */
- List<Object> allDeps = dependencies
- .getUsedOrWasGeneratedByOrWasTriggeredBy();
- // make sure these are processed in the right order: used, wgby, THEN wdf because this latter is derived from the first 2!
- // so collect them into sets and process them separately
-
- Set<WasGeneratedBy> wgbSet = new HashSet<>();
- Set<Used> usedSet = new HashSet<>();
- Set<WasDerivedFrom> wdfSet = new HashSet<>();
- Set<WasControlledBy> wcbSet = new HashSet<>();
- Set<WasTriggeredBy> wtbSet = new HashSet<>();
-
- for (Object dep : allDeps) {
- logger.info("dependency of type: " + dep.getClass().getName());
-
- if (dep instanceof org.openprovenance.model.WasGeneratedBy)
- wgbSet.add((WasGeneratedBy) dep);
- else if (dep instanceof org.openprovenance.model.Used)
- usedSet.add((Used) dep);
- else if (dep instanceof org.openprovenance.model.WasDerivedFrom)
- wdfSet.add((WasDerivedFrom) dep);
- else if (dep instanceof org.openprovenance.model.WasControlledBy)
- wcbSet.add((WasControlledBy) dep);
- else if (dep instanceof org.openprovenance.model.WasTriggeredBy)
- wtbSet.add((WasTriggeredBy) dep);
- }
-
- // process these in the correct order
- for (WasGeneratedBy dep: wgbSet)
- processWGBy(dep);
-
- for (Used dep : usedSet)
- processUsed(dep);
-
- for (WasDerivedFrom dep : wdfSet)
- processWDF(dep);
-
- // we actually ignore the others...
-
- // *********
- // complete the induced graph by building datalinks using the Artifact -> [Port] maps
- // *********
-
- List<String> accountNames = new ArrayList<>();
-
- accountNames.add(OPM_DEF_ACCOUNT);
-
- /* Disabled as allAccounts is never assigned to
- if (allAccounts != null)
- for (Account acc:allAccounts) { accountNames.add(acc.getId()); }
- */
-
- for (String acc : accountNames) {
- String workflowId = accountToWorkflow.get(acc);
-
- Map<String, List<Port>> usedVars = usedVarsByAccount
- .get(workflowId);
- Map<String, List<Port>> wgbVars = wgbVarsByAccount.get(workflowId);
-
- if (usedVars == null || wgbVars == null)
- continue;
-
- // install an Datalink from each wgb var to each used var when the artifact is the same
- for (Map.Entry<String, List<Port>> entry : wgbVars.entrySet()) {
- // all Ports for this artifact get connected to all corresponding Ports in used
- List<Port> sourceVars = entry.getValue();
- List<Port> targetVars = usedVars.get(entry.getKey());
-
- if (sourceVars == null || targetVars == null)
- continue;
-
- // create an datalink from each sourceVar to each targetVar
- // note that we expect a single targetVar, but this is not guaranteed
- for (Port sourceVar : sourceVars)
- for (Port targetVar : targetVars)
- pw.addDataLink(sourceVar, targetVar, workflowId);
- }
- }
- }
-
- private void generateWFFromAccount(String accName) throws SQLException {
- String workflowId = accName + "-" + UUID.randomUUID().toString();
- String workflowRun = accName + "-" + UUID.randomUUID().toString();
-
- pw.addWFId(workflowId);
- pw.addWorkflowRun(workflowId, workflowRun);
- accountToWorkflow.put(accName, workflowId);
- workflowToInstance.put(workflowId, workflowRun);
-
- logger.info("generated workflowId " + workflowId + " and instance "
- + workflowRun + " for account " + accName);
- }
-
- private Port processProcessArtifactDep(String procName, String value,
- String portName, String workflowId, String workflowRun,
- boolean artifactIsInput) {
- // generate Process
- ProvenanceProcessor proc = null;
- try {
- proc = pw.addProcessor(procName, workflowId, false);
- logger.debug("added processor " + procName + " to workflow "
- + workflowId);
- } catch (SQLException e) {
- // no panic -- just catch duplicates
- logger.warn(e.getMessage());
- return null;
- }
-
- // generate Port
- Port outputVar = new Port();
- outputVar.setProcessorId(proc.getIdentifier());
- outputVar.setProcessorName(procName);
- outputVar.setWorkflowId(workflowId);
- outputVar.setPortName(portName);
- outputVar.setDepth(0);
- outputVar.setInputPort(artifactIsInput); // wgby is an output var
-
- List<Port> vars = new ArrayList<>(); // only one Port in the list
- vars.add(outputVar);
-
- try {
- pw.addPorts(vars, workflowId);
- logger.debug("added var "+portName+" to workflow "+workflowId);
- } catch (SQLException e) { // no panic -- just catch duplicates
- logger.warn(e.getMessage());
- }
-
- // generate PortBindings (workflowRun, procName, portName, value)
- PortBinding vb = new PortBinding();
-
- vb.setWorkflowRunId(workflowRun);
- vb.setProcessorName(procName);
- vb.setPortName(portName);
- vb.setValue(value);
- vb.setIteration("[]");
-
- try {
- pw.addPortBinding(vb);
- logger.debug("added var binding with value " + value
- + " to workflow instance " + workflowRun);
- } catch (SQLException e) { // no panic -- just catch duplicates
- logger.error("Failed to add var binding: " + e.getMessage());
- }
-
- return outputVar;
- }
-
- /**
- * generic processing of a process-artifact dependency
- *
- * @param procID
- * @param artId
- * @param role
- * @param workflowId
- * @param workflowRun
- * @param artifactIsInput
- */
- private Port processProcessArtifactDep(ProcessRef procID,
- ArtifactRef artId, Role role, String workflowId,
- String workflowRun, boolean artifactIsInput) {
- String procName = ((Process) procID.getRef()).getId();
- String portName = role.getValue();
- String value = ((Artifact) artId.getRef()).getId();
-
- portName = removeBlanks(portName);
-
- return processProcessArtifactDep(procName, value, portName, workflowId,
- workflowRun, artifactIsInput);
- }
-
- private String removeBlanks(String portName) {
- return portName.replace(" ", "_");
- }
-
- /**
- * used(A,R,P,acc): generates a process for P, a Port for (P,R) an
- * <em>input</em> PortBinding for (P,R,A) <br/>
- * this is very similar to {@link #processWGBy(WasGeneratedBy)}
- *
- * @param dep
- */
- private void processUsed(Used dep) {
- // Acc determines the scope -- this dep may belong to > 1 account, deal with all of them
- List<AccountRef> accountIDs = dep.getAccount();
- ProcessRef procID = dep.getEffect();
- ArtifactRef artId = dep.getCause();
- Role role = dep.getRole();
-
- List<String> accNames = new ArrayList<String>();
-
- for (AccountRef accId : accountIDs)
- accNames.add(((Account) accId.getRef()).getId());
-
- accNames.add(OPM_DEF_ACCOUNT);
-
- for (String accName : accNames) {
- String workflowId = accountToWorkflow.get(accName);
- String workflowRun = workflowToInstance.get(workflowId);
-
- Port v = processProcessArtifactDep(procID, artId, role, workflowId,
- workflowRun, true); // true -> input var
-
- // save the mapping from artifact to var for this account
- Map<String, List<Port>> usedVars = usedVarsByAccount
- .get(workflowId);
- if (usedVars == null) {
- usedVars = new HashMap<>();
- usedVarsByAccount.put(workflowId, usedVars);
- }
- List<Port> vars = usedVars.get(((Artifact) artId.getRef()).getId());
-
- if (vars == null) {
- vars = new ArrayList<>();
- usedVars.put(((Artifact) artId.getRef()).getId(), vars);
- }
- vars.add(v);
-
- // record the fact that (procID used artId) within this account
- Map<String, List<String>> usedArtifacts = usedArtifactsByAccount
- .get(accName);
- if (usedArtifacts == null) {
- usedArtifacts = new HashMap<>();
- usedArtifactsByAccount.put(accName, usedArtifacts);
- }
-
- String artifactName = ((Artifact) artId.getRef()).getId();
- List<String> processes = usedArtifacts.get(artifactName);
- if (processes == null) {
- processes = new ArrayList<>();
- usedArtifacts.put(artifactName, processes);
- }
- processes.add(((org.openprovenance.model.Process) procID.getRef())
- .getId());
- }
- }
-
- /**
- * wgb(A,R,P,Acc): generates a Process for P, a Port for (P,R), an
- * <em>output</em> PortBinding for (P,R,A) This is all relative to the
- * workflow corresponding to account Acc.
- *
- * @param dep
- * @throws SQLException
- */
- private void processWGBy(WasGeneratedBy dep) {
- // Acc determines the scope -- this dep may belong to > 1 account, deal with all of them
- List<AccountRef> accountIDs = dep.getAccount();
- ProcessRef procID = dep.getCause();
- ArtifactRef artId = dep.getEffect();
- Role role = dep.getRole();
-
- List<String> accNames = new ArrayList<String>();
- for (AccountRef accId : accountIDs)
- accNames.add(((Account) accId.getRef()).getId());
- accNames.add(OPM_DEF_ACCOUNT);
-
- for (String accName : accNames) {
- String workflowId = accountToWorkflow.get(accName);
- String workflowRun = workflowToInstance.get(workflowId);
-
- Port v = processProcessArtifactDep(procID, artId, role, workflowId,
- workflowRun, false); // false -> output var
-
- Map<String, List<Port>> wgbVars = wgbVarsByAccount.get(workflowId);
- if (wgbVars == null) {
- wgbVars = new HashMap<>();
- wgbVarsByAccount.put(workflowId, wgbVars);
- }
-
- List<Port> vars = wgbVars.get(((Artifact) artId.getRef()).getId());
- if (vars == null) {
- vars = new ArrayList<>();
- wgbVars.put(((Artifact) artId.getRef()).getId(), vars);
- }
- vars.add(v);
-
- // record the fact that (artId wgby procID) within this account
- Map<String, List<String>> wgbArtifacts = wgbArtifactsByAccount
- .get(accName);
- if (wgbArtifacts == null) {
- wgbArtifacts = new HashMap<>();
- wgbArtifactsByAccount.put(accName, wgbArtifacts);
- }
-
- String artifactName = ((Artifact) artId.getRef()).getId();
- List<String> processes = wgbArtifacts.get(artifactName);
- if (processes == null) {
- processes = new ArrayList<>();
- wgbArtifacts.put(artifactName, processes);
- }
- processes.add(((org.openprovenance.model.Process) procID.getRef())
- .getId());
- }
- }
-
- /**
- * this is a dep between two artifacts A1 and A2. In Taverna we need to
- * postulate the existence of a Process to mediate this dependency. <p/>
- * However, we only need to account for this dep if it cannot be inferred
- * from a combination of used and wgby that involve A1 and A2: if there
- * exists P s.t. A1 wgby P and P used A2, then this dep. is redundant in the
- * DB and we can safely ignore it. <p/>
- * note that this analysis is conducted regardless of the accounts in which
- * the wgby and used properties appear, as one account could be used
- * deliberately to This will unclutter the DB.
- *
- * @param dep
- */
- private void processWDF(WasDerivedFrom dep) {
- List<AccountRef> accountIDs = dep.getAccount();
- ArtifactRef fromArtId = dep.getCause();
- ArtifactRef toArtId = dep.getEffect();
-
- List<String> accNames = new ArrayList<>();
- for (AccountRef accId : accountIDs)
- accNames.add(((Account) accId.getRef()).getId());
- accNames.add(OPM_DEF_ACCOUNT);
-
- for (String accName:accNames) {
- int varCounter = 0;
-
- String workflowId = accountToWorkflow.get(accName);
- String workflowRun = workflowToInstance.get(workflowId);
-
- List<String> generatingProcesses = null, usingProcesses = null;
-
- // look for any triple fromArtId wasGeneratedBy P within this account
- Map<String, List<String>> wgbArtifacts = wgbArtifactsByAccount
- .get(accName);
-
- if (wgbArtifacts != null) {
- String toArtifactName = ((Artifact) toArtId.getRef()).getId();
- generatingProcesses = wgbArtifacts.get(toArtifactName);
- if (generatingProcesses != null)
- logger.debug("artifact " + toArtifactName
- + " wgby one or more processes...");
- }
-
- // look for any triple (P used toArtId) within this account
-
- // get map for this account
- Map<String, List<String>> usedArtifacts = usedArtifactsByAccount
- .get(accName);
-
- if (usedArtifacts != null) {
- String fromArtifactName = ((Artifact) fromArtId.getRef())
- .getId();
- usingProcesses = usedArtifacts.get(fromArtifactName);
- if (usingProcesses != null)
- logger.debug("artifact " + fromArtifactName
- + " was used by one or more processes...");
- }
-
- if (generatingProcesses != null && usingProcesses != null)
- for (String gp : generatingProcesses)
- if (usingProcesses.contains(gp)) {
- logger.debug("intersection between process sets not empty, this WDF is redundant");
- return;
- }
-
- /* We only postulate a new process if the native one was not found */
-
- String procName = PROC_NAME+"_"+procNameCounter++;
-
- try {
- pw.addProcessor(procName, workflowId, false);
- logger.info("created non-native added processor " + procName
- + " to workflow " + workflowId);
- } catch (SQLException e) { // no panic -- just catch duplicates
- logger.warn(e.getMessage());
- }
-
- // create a role for fromArtId from the procName
- String inputPortName = procName + "_" + varCounter++;
- String inputValue = ((Artifact) fromArtId.getRef()).getId();
-
- // add to DB
- processProcessArtifactDep(procName, inputValue, inputPortName,
- workflowId, workflowRun, true);
-
- // create a role for toArtId
- String outputPortName = procName + "_" + varCounter++;
- String outputValue = ((Artifact) toArtId.getRef()).getId();
-
- // add to DB
- processProcessArtifactDep(procName, outputValue, outputPortName,
- workflowId, workflowRun, false);
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/opm/OPMManager.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/opm/OPMManager.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/opm/OPMManager.java
deleted file mode 100644
index a82abdf..0000000
--- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/opm/OPMManager.java
+++ /dev/null
@@ -1,414 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.provenance.opm;
-
-import static org.tupeloproject.rdf.Resource.literal;
-import static org.tupeloproject.rdf.Resource.uriRef;
-
-import java.io.IOException;
-import java.io.StringWriter;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.List;
-
-import net.sf.taverna.t2.provenance.lineageservice.URIGenerator;
-import net.sf.taverna.t2.provenance.lineageservice.utils.DataValueExtractor;
-
-import org.apache.log4j.Logger;
-import org.tupeloproject.kernel.Context;
-import org.tupeloproject.kernel.OperatorException;
-import org.tupeloproject.kernel.UnionContext;
-import org.tupeloproject.kernel.impl.MemoryContext;
-import org.tupeloproject.kernel.impl.ResourceContext;
-import org.tupeloproject.provenance.ProvenanceAccount;
-import org.tupeloproject.provenance.ProvenanceArtifact;
-import org.tupeloproject.provenance.ProvenanceException;
-import org.tupeloproject.provenance.ProvenanceGeneratedArc;
-import org.tupeloproject.provenance.ProvenanceProcess;
-import org.tupeloproject.provenance.ProvenanceRole;
-import org.tupeloproject.provenance.ProvenanceUsedArc;
-import org.tupeloproject.provenance.impl.ProvenanceContextFacade;
-import org.tupeloproject.rdf.Literal;
-import org.tupeloproject.rdf.Resource;
-import org.tupeloproject.rdf.xml.RdfXmlWriter;
-
-
-/**
- * @author paolo
- *
- */
-public class OPMManager {
- private static Logger logger = Logger.getLogger(OPMManager.class);
-
- public static final String OPM_TAVERNA_NAMESPACE = "http://ns.taverna.org.uk/2011/provenance/opm/";
- private static final String VALUE_PROP = "value";
-
- private ProvenanceContextFacade graph = null;
- private Context context = null;
-
- private ProvenanceAccount currentAccount = null;
- private ProvenanceArtifact currentArtifact = null;
- private ProvenanceRole currentRole = null;
- private ProvenanceProcess currentProcess = null;
-
- private boolean isActive = true;
-
- public OPMManager() {
- // init Tupelo RDF provenance graph
- MemoryContext mc = new MemoryContext();
- ResourceContext rc = new ResourceContext("http://example.org/data/",
- "/provenanceExample/");
- context = new UnionContext();
- context.addChild(mc);
- context.addChild(rc);
-
- graph = new ProvenanceContextFacade(mc);
- }
-
- /**
- * default implementation of this method returns null -- has no idea how to
- * extract simple values from incoming artifact values
- *
- * @return
- */
- public List<DataValueExtractor> getDataValueExtractor() {
- return null;
- }
-
- /**
- * create new account to hold the causality graph and give it a Resource
- * name
- *
- * @param accountName
- * @throws ProvenanceException
- */
- public void createAccount(String accountName) throws ProvenanceException {
- currentAccount = graph.newAccount("OPM-" + accountName,
- uriRef(uriGenerator.makeRunUri(accountName)));
- graph.assertAccount(currentAccount);
- }
-
- /**
- * @param aName
- * @param aValue
- * actual value can be used optionally as part of a separate
- * triple. Whether this is used or not depends on the settings,
- * see {@link OPMManager.addValueTriple}. This also sets the
- * currentArtifact to the newly created artifact
- * @throws ProvenanceException
- */
- public void addArtifact(String aName, Object aValue)
- throws ProvenanceException {
- Resource r = addArtifact(aName);
-
- if (aValue == null) {
- logger.debug("OPMManager::addArtifact: aValue for [" + aName
- + "] is NULL");
- return;
- }
-
- logger.debug("OPMManager::addArtifact: aValue is NOT NULL");
-
- // if we have a valid DataValueExtractor, use it here
- List<DataValueExtractor> dveList;
- String extractedValue = (String) aValue; // default is same value
- dveList = getDataValueExtractor();
- if (dveList != null)
- // try all available extractors... UGLY but data comes with NO TYPE at all!
- for (DataValueExtractor dve : dveList)
- try {
- logger.debug("OPMManager::addArtifact: trying extractor "
- + dve.getClass().getName());
- extractedValue = dve.extractString(aValue);
- logger.debug("OPMManager::addArtifact: - extracted value = "
- + extractedValue);
- break; // extractor worked
- } catch (Exception e) {
- // no panic, reset value and try another extractor
- logger.warn("OPMManager::addArtifact: extractor failed");
- extractedValue = (String) aValue;
- }
-
- logger.debug("OPMManager::addArtifact: using value " + extractedValue);
- try {
- Literal lValue = literal(extractedValue);
- context.addTriple(r, uriRef(OPM_TAVERNA_NAMESPACE + VALUE_PROP),
- lValue);
- } catch (OperatorException e) {
- logger.warn("OPM iteration triple creation exception", e);
- }
- }
-
- /**
- * no actual value is recorded
- *
- * @param aName
- * @return
- * @throws ProvenanceException
- */
- public Resource addArtifact(String aName) throws ProvenanceException {
- String artID = null;
- // make sure artifact name is a good URI
- try {
- URI artURI = new URI(aName);
- if (artURI.getScheme() != null) {
- if (artURI.getScheme().equals("t2"))
- artID = uriGenerator.makeT2ReferenceURI(aName);
- else
- artID = aName;
- }
- } catch (URISyntaxException e1) {
- // generate later
- }
- if (artID == null)
- artID = OPM_TAVERNA_NAMESPACE + "artifact/"
- + uriGenerator.escape(aName);
-
- Resource r = uriRef(artID);
- currentArtifact = graph.newArtifact(artID, r);
- graph.assertArtifact(currentArtifact);
- return r;
- }
-
- public void createRole(String workflowRunId, String workflowId,
- String processorName, String iteration) {
- String aRole = uriGenerator.makeIteration(workflowRunId, workflowId,
- processorName, iteration);
- Resource r = Resource.uriRef(aRole);
- currentRole = graph.newRole(aRole, r);
- }
-
- private URIGenerator uriGenerator = new URIGenerator();
-
- public void addProcess(String processorName, String iterationVector,
- String workflowId, String workflowRunId) throws ProvenanceException {
- String processID;
-
- /*
- * PM added 5/09 -- a process name may already be a URI -- this happens
- * for example when we export back OPM after importing a workflow from
- * our own OPM... in this case, do not pre-pend a new URI scheme
- */
- try {
- URI procURI = new URI(processorName);
-
- if (procURI.getAuthority() == null) {
- processID = uriGenerator.makeProcessorURI(processorName, workflowId);
- } else {
- processID = processorName;
- }
- } catch (URISyntaxException e1) {
- processID = uriGenerator.makeProcessorURI(processorName, workflowId);
- }
-
- uriGenerator.makeIteration(workflowRunId, workflowId, processorName,
- iterationVector);
-
- Resource processResource = uriRef(processID);
- currentProcess = graph.newProcess(processID, processResource);
- graph.assertProcess(currentProcess);
-
- /*
- * add a triple to specify the iteration vector for this occurrence of
- * Process, if it is available
- */
- try {
- if (! iterationVector.equals("[]"))
- // Resource inputProcessSubject = ((RdfProvenanceProcess) process).getSubject();
- context.addTriple(processResource, uriRef(OPM_TAVERNA_NAMESPACE
- + "iteration"), iterationVector);
- } catch (OperatorException e) {
- logger.warn("OPM iteration triple creation exception", e);
- }
- }
-
- public void assertGeneratedBy(ProvenanceArtifact artifact,
- ProvenanceProcess process, ProvenanceRole role,
- ProvenanceAccount account, boolean noDuplicates)
- throws ProvenanceException {
- boolean found = false;
- if (noDuplicates && artifact != null)
- for (ProvenanceGeneratedArc datalink : graph
- .getGeneratedBy(artifact)) {
- ProvenanceProcess pp = datalink.getProcess();
- if (pp.getName().equals(process.getName())) {
- found = true;
- break;
- }
- }
-
- if (!noDuplicates || (noDuplicates && !found) && artifact != null)
- graph.assertGeneratedBy(artifact, process, role, account);
- }
-
- public void assertUsed(ProvenanceArtifact artifact,
- ProvenanceProcess process, ProvenanceRole role,
- ProvenanceAccount account, boolean noDuplicates)
- throws ProvenanceException {
- boolean found = false;
-
- if (noDuplicates)
- for (ProvenanceUsedArc datalink : graph.getUsed(process)) {
- ProvenanceArtifact pa = datalink.getArtifact();
- if (pa.getName().equals(artifact.getName())) {
- found = true;
- break;
- }
- }
-
- if (!noDuplicates || (noDuplicates && !found))
- graph.assertUsed(process, artifact, role, account);
- }
-
- public ProvenanceContextFacade getGraph() {
- return graph;
- }
-
- /**
- * @return the account
- */
- public ProvenanceAccount getAccount() {
- return currentAccount;
- }
-
- /**
- * @param account
- * the account to set
- */
- public void setAccount(ProvenanceAccount account) {
- this.currentAccount = account;
- }
-
- /**
- * @return the currentRole
- */
- public ProvenanceRole getCurrentRole() {
- return currentRole;
- }
-
- /**
- * @param currentRole
- * the currentRole to set
- */
- public void setCurrentRole(ProvenanceRole currentRole) {
- this.currentRole = currentRole;
- }
-
- /**
- * @return the currentArtifact
- */
- public ProvenanceArtifact getCurrentArtifact() {
- return currentArtifact;
- }
-
- /**
- * @param currentArtifact
- * the currentArtifact to set
- */
- public void setCurrentArtifact(ProvenanceArtifact currentArtifact) {
- this.currentArtifact = currentArtifact;
- }
-
- /**
- * @return the currentAccount
- */
- public ProvenanceAccount getCurrentAccount() {
- return currentAccount;
- }
-
- /**
- * @param currentAccount
- * the currentAccount to set
- */
- public void setCurrentAccount(ProvenanceAccount currentAccount) {
- this.currentAccount = currentAccount;
- }
-
- /**
- * @return the currentProcess
- */
- public ProvenanceProcess getCurrentProcess() {
- return currentProcess;
- }
-
- /**
- * @param currentProcess
- * the currentProcess to set
- */
- public void setCurrentProcess(ProvenanceProcess currentProcess) {
- this.currentProcess = currentProcess;
- }
-
- public String writeGraph() {
- // print out OPM graph in RDF/XML form
- try {
- StringWriter sw = new StringWriter();
- new RdfXmlWriter().write(context.getTriples(), sw);
- return sw.toString();
- } catch (OperatorException | IOException e) {
- logger.error("Could not write graph", e);
- }
- return null;
- }
-
- /**
- * IN THE RELEASE WE DO NOT SUPPORT XML -- ONE CAN CONVERT THE RDF TO XML OUT-OF-BAND
- * simply invokes the org.openprovenance for converting an RDF OPM graph to an XML OPM graph
- * @return a hard-coded filename for the converted XML OPM graph
- * @throws OperatorException
- * @throws IOException
- * @throws JAXBException
- */
-// public String Rdf2Xml() throws OperatorException, IOException, JAXBException {
-//
-// OPMRdf2Xml converter = new OPMRdf2Xml();
-// converter.convert(OPM_RDF_GRAPH_FILE, OPM_XML_GRAPH_FILE);
-// return OPM_XML_GRAPH_FILE;
-// }
-
- /**
- * creates a dot file from the current OPMGraph. <br/>
- * DOT NOT USE NEEDS FIXING
- * @return
- * @throws IOException
- * @throws OperatorException
- */
- /*
- public String Rdf2Dot() throws OperatorException, IOException {
-
- OPMRdf2Xml converter = new OPMRdf2Xml();
- OPMGraph graph = converter.convert(OPM_RDF_GRAPH_FILE);
-
- List<Process> processes = graph.getProcesses().getProcess();
- for (Process p:processes) { p.setId("\""+p.getId()+"\""); }
-
- List<Artifact> artifacts = graph.getArtifacts().getArtifact();
- for (Artifact a:artifacts) { a.setId("\""+a.getId()+"\""); }
-
-// OPMToDot aOPMToDot = new OPMToDot(DOT_CONFIG_FILE);
- OPMToDot aOPMToDot = new OPMToDot();
-
- aOPMToDot.convert(graph, new File(OPM_DOT_FILE));
- return OPM_DOT_FILE;
-
- }
-
- */
-
- /**
- * @param graph
- * the graph to set
- */
- public void setGraph(ProvenanceContextFacade graph) {
- this.graph = graph;
- }
-
- public void setActive(boolean active) {
- isActive = active;
- }
-
- public boolean isActive() {
- return isActive;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-provenanceconnector/src/main/resources/META-INF/spring/provenance-connector-context.xml
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/resources/META-INF/spring/provenance-connector-context.xml b/taverna-provenanceconnector/src/main/resources/META-INF/spring/provenance-connector-context.xml
deleted file mode 100644
index 2a4b3c0..0000000
--- a/taverna-provenanceconnector/src/main/resources/META-INF/spring/provenance-connector-context.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:osgi="http://www.springframework.org/schema/osgi"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <bean id="ProvenanceAccess" class="net.sf.taverna.t2.provenance.api.ProvenanceAccess">
- <property name="referenceService" ref="referenceService" />
- <property name="provenanceConnector" ref="provenanceConnector" />
- </bean>
-
- <osgi:service ref="ProvenanceAccess" interface="net.sf.taverna.t2.provenance.Provenance"/>
-
- <osgi:reference id="referenceService" interface="net.sf.taverna.t2.reference.ReferenceService"/>
- <osgi:reference id="provenanceConnector" interface="net.sf.taverna.t2.provenance.reporter.ProvenanceReporter"/>
-</beans>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-provenanceconnector/src/main/resources/janus.owl
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/resources/janus.owl b/taverna-provenanceconnector/src/main/resources/janus.owl
deleted file mode 100644
index 1017574..0000000
--- a/taverna-provenanceconnector/src/main/resources/janus.owl
+++ /dev/null
@@ -1 +0,0 @@
-/Users/paolo/Dropbox/Janus/janus.owl
\ No newline at end of file