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Posted to commits@taverna.apache.org by st...@apache.org on 2016/06/06 12:00:57 UTC
[2/2] incubator-taverna-engine git commit: Removed (C) Univ of
Manchester copyright statements
Removed (C) Univ of Manchester copyright statements
As this code was part of apache-import-20150223 covered
by the Software Grant, it should have ASF file headers.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/commit/7fc503c9
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/tree/7fc503c9
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/diff/7fc503c9
Branch: refs/heads/master
Commit: 7fc503c924f3c11f0b4a86c851c66ba1774f92ba
Parents: 113871b
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Jun 6 13:00:01 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Jun 6 13:00:01 2016 +0100
----------------------------------------------------------------------
.../apache/taverna/provenance/Provenance.java | 28 +++----
.../provenance/ProvenanceConnectorFactory.java | 8 +-
.../taverna/provenance/api/NativeAnswer.java | 13 +--
.../provenance/api/ProvenanceAccess.java | 54 ++++---------
.../provenance/api/ProvenanceConnectorType.java | 15 +---
.../apache/taverna/provenance/api/Query.java | 12 +--
.../taverna/provenance/api/QueryAnswer.java | 15 ++--
.../connector/AbstractProvenanceConnector.java | 28 +------
.../provenance/connector/ProvenanceSQL.java | 7 +-
.../lineageservice/AnnotationsLoader.java | 30 +------
.../provenance/lineageservice/Dependencies.java | 40 +++-------
.../lineageservice/EventProcessor.java | 34 ++------
.../LineageQueryResultRecord.java | 36 ++-------
.../lineageservice/LineageSQLQuery.java | 33 ++------
.../provenance/lineageservice/Provenance.java | 58 +++++---------
.../lineageservice/ProvenanceAnalysis.java | 84 ++++++++------------
.../lineageservice/ProvenanceQuery.java | 30 +------
.../lineageservice/ProvenanceWriter.java | 50 ++++--------
.../provenance/lineageservice/URIGenerator.java | 14 ++--
.../lineageservice/WorkflowDataProcessor.java | 41 +++++-----
.../lineageservice/types/ActivityType.java | 40 +++-------
.../lineageservice/types/DataDocumentType.java | 39 +++------
.../lineageservice/types/IterationType.java | 44 +++-------
.../lineageservice/types/LiteralType.java | 36 ++-------
.../lineageservice/types/PortType.java | 43 +++-------
.../lineageservice/types/PortsSequenceType.java | 36 ++-------
.../lineageservice/types/ProcessType.java | 44 +++-------
.../lineageservice/types/ProcessorType.java | 39 +++------
.../types/ProvenanceEventType.java | 29 +------
.../lineageservice/utils/Activity.java | 8 +-
.../lineageservice/utils/Collection.java | 8 +-
.../lineageservice/utils/DDRecord.java | 15 ++--
.../lineageservice/utils/DataBinding.java | 8 +-
.../lineageservice/utils/DataLink.java | 33 +-------
.../utils/DataValueExtractor.java | 17 +---
.../utils/DataflowInvocation.java | 8 +-
.../lineageservice/utils/NestedListNode.java | 15 +---
.../provenance/lineageservice/utils/Port.java | 30 +------
.../lineageservice/utils/PortBinding.java | 32 +-------
.../lineageservice/utils/ProcessorBinding.java | 32 +-------
.../utils/ProcessorEnactment.java | 8 +-
.../utils/ProvenanceProcessor.java | 30 +------
.../lineageservice/utils/ProvenanceUtils.java | 16 ++--
.../lineageservice/utils/QueryPort.java | 15 +---
.../lineageservice/utils/ServiceInvocation.java | 8 +-
.../lineageservice/utils/Workflow.java | 12 ++-
.../lineageservice/utils/WorkflowRun.java | 9 +--
.../lineageservice/utils/WorkflowTree.java | 13 +--
.../taverna/provenance/opm/OPMImporter.java | 31 +++-----
.../taverna/provenance/opm/OPMManager.java | 35 ++++----
50 files changed, 356 insertions(+), 1007 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/Provenance.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/Provenance.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/Provenance.java
index 309e2b2..d10a7a7 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/Provenance.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/Provenance.java
@@ -1,5 +1,3 @@
-package org.apache.taverna.provenance;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -8,9 +6,9 @@ package org.apache.taverna.provenance;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -18,7 +16,7 @@ package org.apache.taverna.provenance;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance;
import java.sql.SQLException;
import java.util.List;
@@ -58,7 +56,7 @@ import org.apache.taverna.reference.T2Reference;
* <p/>
* The XML schema for the XML query language is {@code pquery.xsd} in
* {@link net.sf.taverna.t2.provenance.apic.client.resources}
- *
+ *
* @author Paolo Missier
* @author Stuart Owen
*/
@@ -96,7 +94,7 @@ public interface Provenance {
* This is used in the workbench to retrieve the "intermediate results" at
* various points during workflow execution, as opposed to a set of
* dependencies in response to a full-fledged provenance query.
- *
+ *
* @param workflowRunId
* lineage scope -- a specific instance
* @param processorName
@@ -139,7 +137,7 @@ public interface Provenance {
/**
* Removes all records that pertain to a specific run (but not the static
* specification of the workflow run)
- *
+ *
* @param runID
* the internal ID of a run. This can be obtained using
* {@link #listRuns(String, Map)}
@@ -151,7 +149,7 @@ public interface Provenance {
/**
* removes all records pertaining to the static structure of a workflow.
- *
+ *
* @param workflowId
* the ID (not the external name) of the workflow whose static
* structure is to be deleted from the DB
@@ -162,7 +160,7 @@ public interface Provenance {
* returns a set of workflowIDs for a given runID. The set is a singleton if
* the workflow has no nesting, but in general the list contains one
* workflowID for each nested workflow involved in the run
- *
+ *
* @param runID
* the internal ID for a specific workflow run
* @return a list of workflow IDs, one for each nested workflow involved in
@@ -203,7 +201,7 @@ public interface Provenance {
/**
* lists all ports for a workflow
- *
+ *
* @param workflowID
* @return a list of {@link Port} beans, each representing an input or
* output port for the workflow
@@ -212,7 +210,7 @@ public interface Provenance {
/**
* lists all ports for a workflow
- *
+ *
* @param workflowID
* @return a list of {@link Port} beans, each representing an input or
* output port for the workflow or a processor in the workflow
@@ -221,7 +219,7 @@ public interface Provenance {
/**
* list all ports for a specific processor within a workflow
- *
+ *
* @param workflowID
* @param processorName
* @return a list of {@link Port} beans, each representing an input or
@@ -257,7 +255,7 @@ public interface Provenance {
void toggleOPMGeneration(boolean active);
/**
- *
+ *
* @return true if OPM is set to be generated in response to a query
*/
boolean isOPMGenerationActive();
@@ -266,7 +264,7 @@ public interface Provenance {
* should actual artifact values be attached to OPM artifact nodes?<br>
* default is FALSE<br/>
* THIS IS CURRENTLY UNSUPPORTED -- DEFAULTS TO FALSE
- *
+ *
* @param active
*/
void toggleAttachOPMArtifactValues(boolean active);
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/ProvenanceConnectorFactory.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/ProvenanceConnectorFactory.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/ProvenanceConnectorFactory.java
index 351ec9c..acb5573 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/ProvenanceConnectorFactory.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/ProvenanceConnectorFactory.java
@@ -1,5 +1,3 @@
-package org.apache.taverna.provenance;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -8,9 +6,9 @@ package org.apache.taverna.provenance;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -18,7 +16,7 @@ package org.apache.taverna.provenance;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance;
import org.apache.taverna.provenance.connector.AbstractProvenanceConnector;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/NativeAnswer.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/NativeAnswer.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/NativeAnswer.java
index 051defb..d181c19 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/NativeAnswer.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/NativeAnswer.java
@@ -1,8 +1,3 @@
-/**
- *
- */
-package org.apache.taverna.provenance.api;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -11,9 +6,9 @@ package org.apache.taverna.provenance.api;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -21,7 +16,7 @@ package org.apache.taverna.provenance.api;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.api;
import java.util.List;
import java.util.Map;
@@ -34,7 +29,7 @@ import org.apache.taverna.provenance.lineageservice.LineageQueryResultRecord;
* Java bean used to encapsulate the results of a provenance query. <br/>
* This takes the form of a nested map, see {@link #getAnswer} for details on
* its structure.
- *
+ *
* @author Paolo Missier
*/
public class NativeAnswer {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java
index 1b0caa6..d1091fc 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceAccess.java
@@ -1,26 +1,3 @@
-/*******************************************************************************
- * Copyright (C) 2009 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 org.apache.taverna.provenance.api;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -29,9 +6,9 @@ package org.apache.taverna.provenance.api;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -40,6 +17,7 @@ package org.apache.taverna.provenance.api;
* under the License.
*/
+package org.apache.taverna.provenance.api;
import static java.sql.Connection.TRANSACTION_READ_UNCOMMITTED;
import static javax.naming.Context.INITIAL_CONTEXT_FACTORY;
@@ -93,7 +71,7 @@ import org.apache.log4j.Logger;
* <p/>
* The XML schema for the XML query language is {@code pquery.xsd} in
* {@link net.sf.taverna.t2.provenance.apic.client.resources}
- *
+ *
* @author Paolo Missier
* @author Stuart Owen
*/
@@ -104,7 +82,7 @@ public class ProvenanceAccess implements Provenance {
private ProvenanceAnalysis analyser = null;
private ProvenanceQuery querier;
private ProvenanceWriter writer;
-
+
private String connectorType;
private final List<ProvenanceConnectorFactory> provenanceConnectorFactories;
@@ -127,7 +105,7 @@ public class ProvenanceAccess implements Provenance {
* name and jdbc url are required.<p/>
* If the driver supports multiple connections, then a pool will be created
* of 10 min idle, 50 max idle, and 50 max active connections.
- *
+ *
* @param driverClassName
* @param jdbcUrl
*/
@@ -138,7 +116,7 @@ public class ProvenanceAccess implements Provenance {
/**
* Initialises a named JNDI DataSource if not already set up externally. The
* DataSource is named jdbc/taverna
- *
+ *
* @param driverClassName
* - the classname for the driver to be used.
* @param jdbcUrl
@@ -268,7 +246,7 @@ public class ProvenanceAccess implements Provenance {
* This is used in the workbench to retrieve the "intermediate results" at
* various points during workflow execution, as opposed to a set of
* dependencies in response to a full-fledged provenance query.
- *
+ *
* @param workflowRunId
* lineage scope -- a specific instance
* @param processorName
@@ -349,7 +327,7 @@ public class ProvenanceAccess implements Provenance {
/**
* Removes all records that pertain to a specific run (but not the static
* specification of the workflow run)
- *
+ *
* @param runID
* the internal ID of a run. This can be obtained using
* {@link #listRuns(String, Map)}
@@ -376,7 +354,7 @@ public class ProvenanceAccess implements Provenance {
/**
* removes all records pertaining to the static structure of a workflow.
- *
+ *
* @param workflowId
* the ID (not the external name) of the workflow whose static
* structure is to be deleted from the DB
@@ -394,7 +372,7 @@ public class ProvenanceAccess implements Provenance {
* returns a set of workflowIDs for a given runID. The set is a singleton if
* the workflow has no nesting, but in general the list contains one
* workflowID for each nested workflow involved in the run
- *
+ *
* @param runID
* the internal ID for a specific workflow run
* @return a list of workflow IDs, one for each nested workflow involved in
@@ -478,7 +456,7 @@ public class ProvenanceAccess implements Provenance {
/**
* lists all ports for a workflow
- *
+ *
* @param workflowID
* @return a list of {@link Port} beans, each representing an input or
* output port for the workflow
@@ -490,7 +468,7 @@ public class ProvenanceAccess implements Provenance {
/**
* lists all ports for a workflow
- *
+ *
* @param workflowID
* @return a list of {@link Port} beans, each representing an input or
* output port for the workflow or a processor in the workflow
@@ -502,7 +480,7 @@ public class ProvenanceAccess implements Provenance {
/**
* list all ports for a specific processor within a workflow
- *
+ *
* @param workflowID
* @param processorName
* @return a list of {@link Port} beans, each representing an input or
@@ -572,7 +550,7 @@ public class ProvenanceAccess implements Provenance {
}
/**
- *
+ *
* @return true if OPM is set to be generated in response to a query
*/
@Override
@@ -584,7 +562,7 @@ public class ProvenanceAccess implements Provenance {
* should actual artifact values be attached to OPM artifact nodes?<br>
* default is FALSE<br/>
* THIS IS CURRENTLY UNSUPPORTED -- DEFAULTS TO FALSE
- *
+ *
* @param active
*/
@Override
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceConnectorType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceConnectorType.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceConnectorType.java
index e6ff8e1..ec9fec7 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceConnectorType.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceConnectorType.java
@@ -1,11 +1,4 @@
/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
-
-package org.apache.taverna.provenance.api;
-
-/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
@@ -13,9 +6,9 @@ package org.apache.taverna.provenance.api;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -23,11 +16,11 @@ package org.apache.taverna.provenance.api;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.api;
/**
* Defines names for the common Provenance Connector types
- *
+ *
* @author Stuart Owen
*/
public class ProvenanceConnectorType {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/Query.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/Query.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/Query.java
index 0f09f98..b0f4225 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/Query.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/Query.java
@@ -1,7 +1,3 @@
-/**
- *
- */
-package org.apache.taverna.provenance.api;
/*
* Licensed to the Apache Software Foundation (ASF) under one
@@ -11,9 +7,9 @@ package org.apache.taverna.provenance.api;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -21,7 +17,7 @@ package org.apache.taverna.provenance.api;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.api;
import java.util.List;
@@ -38,7 +34,7 @@ import org.apache.taverna.provenance.lineageservice.utils.QueryPort;
* <li>a list of <target> processors, encoded as List<
* {@link ProvenanceProcessor}>
* </ul>
- *
+ *
* @author Paolo Missier
*/
public class Query {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/QueryAnswer.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/QueryAnswer.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/QueryAnswer.java
index d87e929..e8e244e 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/QueryAnswer.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/QueryAnswer.java
@@ -1,8 +1,3 @@
-/**
- *
- */
-package org.apache.taverna.provenance.api;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -11,9 +6,9 @@ package org.apache.taverna.provenance.api;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -21,14 +16,16 @@ package org.apache.taverna.provenance.api;
* specific language governing permissions and limitations
* under the License.
*/
+package org.apache.taverna.provenance.api;
+
/**
* Encapsulates a native Java data structure as a well as a String that holds
* the OPM graph that represents the query answer
- *
+ *
* @author Paolo Missier
- *
+ *
*/
public class QueryAnswer {
private NativeAnswer nativeAnswer;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/AbstractProvenanceConnector.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/AbstractProvenanceConnector.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/AbstractProvenanceConnector.java
index c026ffc..9825bcb 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/AbstractProvenanceConnector.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/AbstractProvenanceConnector.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.connector;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.connector;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,7 +16,7 @@ package org.apache.taverna.provenance.connector;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.connector;
import java.io.IOException;
import java.sql.Connection;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/ProvenanceSQL.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/ProvenanceSQL.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/ProvenanceSQL.java
index 9c76169..8419563 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/ProvenanceSQL.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/ProvenanceSQL.java
@@ -1,5 +1,3 @@
-package org.apache.taverna.provenance.connector;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -8,9 +6,9 @@ package org.apache.taverna.provenance.connector;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -19,6 +17,7 @@ package org.apache.taverna.provenance.connector;
* under the License.
*/
+package org.apache.taverna.provenance.connector;
public class ProvenanceSQL {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/AnnotationsLoader.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/AnnotationsLoader.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/AnnotationsLoader.java
index 8afa84e..a46089d 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/AnnotationsLoader.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/AnnotationsLoader.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import java.io.FileReader;
import java.io.IOException;
@@ -55,7 +33,7 @@ import org.jdom.input.SAXBuilder;
/**
* @author Paolo Missier
- *
+ *
*/
public class AnnotationsLoader {
private static Logger logger = Logger.getLogger(AnnotationsLoader.class);
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Dependencies.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Dependencies.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Dependencies.java
index 5078419..4f4596c 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Dependencies.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Dependencies.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import java.util.ArrayList;
import java.util.List;
@@ -49,14 +27,14 @@ import java.util.ListIterator;
* one record in the provenance DB at the finest possible level of granularity,
* i.e., a single value possibly within a collection, bound to a processor port
* and associated to a specific run of a specific workflow.
- *
+ *
* @author Paolo Missier
* @see LineageQueryResultRecord
*/
public class Dependencies {
final public static String COLL_TYPE = "referenceSetCollection";
final public static String ATOM_TYPE = "referenceSet";
-
+
boolean printResolvedValue;
private List<LineageQueryResultRecord> records = new ArrayList<>();
@@ -67,7 +45,7 @@ public class Dependencies {
/**
* adds a single record to the list of dependencies
- *
+ *
* @param workflowId
* @param pname
* @param vname
@@ -125,13 +103,13 @@ public class Dependencies {
for (LineageQueryResultRecord record : getRecords()) {
record.setPrintResolvedValue(printResolvedValue);
sb.append("*** record: ****\n"+record.toString());
- }
+ }
return sb.toString();
}
/**
* @return true is the records contain the actual values, in addition to the URI references to the values
- * <br/>NOT YET SUPPORTED. This switch is currently ignored and no values are returned in the current version
+ * <br/>NOT YET SUPPORTED. This switch is currently ignored and no values are returned in the current version
*/
public boolean isPrintResolvedValue() {
return printResolvedValue;
@@ -139,7 +117,7 @@ public class Dependencies {
/**
* @param toggles insertion of values in addition to references to values in the records
- * <br/>NOT YET SUPPORTED. This switch is currently ignored and no values are returned in the current version
+ * <br/>NOT YET SUPPORTED. This switch is currently ignored and no values are returned in the current version
*/
public void setPrintResolvedValue(boolean printResolvedValue) {
this.printResolvedValue = printResolvedValue;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/EventProcessor.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/EventProcessor.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/EventProcessor.java
index d793d4e..fcb8224 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/EventProcessor.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/EventProcessor.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import static java.util.Collections.synchronizedList;
import static org.apache.taverna.provenance.lineageservice.utils.ProvenanceProcessor.DATAFLOW_ACTIVITY;
@@ -282,7 +260,7 @@ public class EventProcessor {
/**
* note: this method can be called as part of a recursion on sub-workflows
- *
+ *
* @param df
* @param dataflowID
* the UUID for the entire dataflow (may be a sub-dataflow)
@@ -539,7 +517,7 @@ public class EventProcessor {
case PROCESS_EVENT_TYPE: {
String parentId = provenanceItem.getParentId(); // this is the workflowID
String identifier = provenanceItem.getIdentifier(); // use this as workflowRunId if this is the top-level process
-
+
parentChildMap.put(identifier, parentId);
ProcessorBinding pb = new ProcessorBinding();
pb.setWorkflowRunId(getWorkflowRunId());
@@ -1005,7 +983,7 @@ public class EventProcessor {
* Conversely, if vb is going to be input to an iteration, then it's lost
* its containing list node, and we put it back in by looking at the
* corresponding predecessor
- *
+ *
* @param vb
* @throws SQLException
*/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageQueryResultRecord.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageQueryResultRecord.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageQueryResultRecord.java
index 20ccc0d..426bcc0 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageQueryResultRecord.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageQueryResultRecord.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,10 +16,10 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
/**
- *
+ *
* This Java bean holds a single provenance record, i.e., the finest element of
* a provenance graph that is stored in the provenance DB. Essentially this
* represents one data element (value) flowing through a port (vname) of a
@@ -50,9 +28,9 @@ package org.apache.taverna.provenance.lineageservice;
* same processor receives multiple values on the same port, as part of
* iterative processing. When the value belongs to a collection (a nested list),
* the <b>collIdRef</b> field contains a reference to that collection.
- *
+ *
* @author Paolo Missier
- *
+ *
*/
public class LineageQueryResultRecord {
private String workflowId;
@@ -66,7 +44,7 @@ public class LineageQueryResultRecord {
private String resolvedValue;
private String type; // one of referenceSet, referenceSetCollection
boolean printResolvedValue;
- boolean isInput;
+ boolean isInput;
boolean isCollection;
@Override
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageSQLQuery.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageSQLQuery.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageSQLQuery.java
index 5605187..c82d8ca 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageSQLQuery.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/LineageSQLQuery.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,6 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
+package org.apache.taverna.provenance.lineageservice;
/**
@@ -46,9 +25,9 @@ package org.apache.taverna.provenance.lineageservice;
* relevant. For instance when the query includes a join with Collection, the
* intent is that lineage should return the collection itself as opposed to any
* of its elements.
- *
+ *
* @author paolo
- *
+ *
*/
public class LineageSQLQuery {
private String vbQuery = null;
@@ -98,5 +77,5 @@ public class LineageSQLQuery {
*/
public void setVbQuery(String vbQuery) {
this.vbQuery = vbQuery;
- }
+ }
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Provenance.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Provenance.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Provenance.java
index c012376..498e891 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Provenance.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/Provenance.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import java.io.IOException;
import java.sql.SQLException;
@@ -59,10 +37,10 @@ import org.apache.log4j.Logger;
/**
* Implemented by the database class that a {@link AbstractProvenanceConnector}
* implementation uses for storage purposes
- *
+ *
* @author Paolo Missier
* @author Ian Dunlop
- *
+ *
*/
//FIXME is this class really needed. Can't we just push the
//acceptRawProvanceEvent up into the ProvenanceConnector?
@@ -74,7 +52,7 @@ public class Provenance {
protected EventProcessor ep;
private String saveEvents;
-
+
private volatile boolean firstWorkflowStructure = true;
public boolean isFirstWorkflowStructure() {
@@ -86,7 +64,7 @@ public class Provenance {
}
private List<String> workflowIDStack = Collections.synchronizedList(new ArrayList<String>());
-
+
private Map<String, String> workflowIDMap = new ConcurrentHashMap<String, String>();
public Provenance() { }
@@ -94,14 +72,14 @@ public class Provenance {
public Provenance(EventProcessor eventProcessor) {
this.ep = eventProcessor;
this.pq = ep.getPq();
- this.pw = ep.getPw();
+ this.pw = ep.getPw();
}
public void clearDB() throws SQLException {
getPw().clearDBStatic();
getPw().clearDBDynamic();
}
-
+
/**
* @return the saveEvents
@@ -147,7 +125,7 @@ public class Provenance {
/**
* maps each incoming event to an insert query into the provenance store
- *
+ *
* @param eventType
* @param content
* @throws SQLException
@@ -160,7 +138,7 @@ public class Provenance {
/**
* parse d and generate SQL insert calls into the provenance DB
- *
+ *
* @param d
* DOM for the event
* @param eventType
@@ -174,24 +152,24 @@ public class Provenance {
// process the workflow structure
//workflowStartedMap.put()
WorkflowProvenanceItem workflowProvenanceItem = (WorkflowProvenanceItem) provenanceItem;
-
+
getEp().getWfdp().workflowStarted.put(workflowProvenanceItem.getIdentifier(), workflowProvenanceItem.getInvocationStarted());
if (isFirstWorkflowStructure()) {
String dataflowId = workflowProvenanceItem.getDataflow().getIdentifier();
String instanceId = provenanceItem.getIdentifier();
-
+
workflowIDMap.put(instanceId, dataflowId);
setFirstWorkflowStructure(false);
String processWorkflowStructure = getEp().processWorkflowStructure(provenanceItem);
synchronized(workflowIDStack) {
workflowIDStack.add(0,processWorkflowStructure);
}
-
+
getEp().propagateANL(provenanceItem.getIdentifier());
} else {
String dataflowId = workflowProvenanceItem.getDataflow().getIdentifier();
String instanceId = provenanceItem.getIdentifier();
-
+
workflowIDMap.put(instanceId, dataflowId);
Dataflow df = workflowProvenanceItem.getDataflow();
@@ -203,16 +181,16 @@ public class Provenance {
// String currentWorkflowID = workflowIDStack.get(0);
// workflowIDStack.remove(0);
String currentWorkflowID = provenanceItem.getParentId();
-
+
getEp().processProcessEvent(provenanceItem, currentWorkflowID);
-
+
} else { // all other event types (iteration etc.)
logger.debug("processEvent of type "+provenanceItem.getEventType()+" for item of type "+provenanceItem.getClass().getName());
String currentWorkflowID = provenanceItem.getWorkflowId();
// String currentWorkflowID = workflowIDMap.get(provenanceItem.getParentId());
getEp().processProcessEvent(provenanceItem, currentWorkflowID);
-
+
// getEp().processProcessEvent(provenanceItem, workflowIDStack.get(0));
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceAnalysis.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceAnalysis.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceAnalysis.java
index cceed34..b636af0 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceAnalysis.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceAnalysis.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import java.io.IOException;
import java.sql.SQLException;
@@ -150,7 +128,7 @@ public class ProvenanceAnalysis {
/**
- * asks the OPM manager to convert its current RDF OPMGraph to XML
+ * asks the OPM manager to convert its current RDF OPMGraph to XML
* @return the filename of the OPM XML file
* @throws OperatorException
* @throws IOException
@@ -159,7 +137,7 @@ public class ProvenanceAnalysis {
// public String OPMRdf2Xml() throws OperatorException, IOException, JAXBException {
// if (isReady()) {
// return aOPMManager.Rdf2Xml();
- // }
+ // }
// return null;
// }
@@ -167,15 +145,15 @@ public class ProvenanceAnalysis {
* asks the OPM manager to create a dot file representing its current RDF OPMGraph<br/>
* needs fixing
* @return
- * @throws IOException
- * @throws OperatorException
+ * @throws IOException
+ * @throws OperatorException
*/
/*
public String OPMRdf2Dot() throws OperatorException, IOException {
if (aOPMManager != null && aOPMManager.isActive() && isReady()) {
return aOPMManager.Rdf2Dot();
- }
- return null;
+ }
+ return null;
}
*/
@@ -196,7 +174,7 @@ public class ProvenanceAnalysis {
/**
* returns all available instances across all workflows
- *
+ *
* @return
* @throws SQLException
*/
@@ -206,7 +184,7 @@ public class ProvenanceAnalysis {
/**
* returns all available instances for workflow workflowId
- *
+ *
* @param workflowId
* @return
* @throws SQLException
@@ -256,7 +234,7 @@ public class ProvenanceAnalysis {
// launch a lineage query for each target variable
for (QueryPort qv : qvList) {
- // full lineage query
+ // full lineage query
logger.info(String.format(
"************\n lineage query: [instance, workflow, proc, port, path] = "
+ "[%s,%s,%s,%s,[%s]]\n***********", workflowRun,
@@ -302,7 +280,7 @@ public class ProvenanceAnalysis {
* is specified, however, this just passes the request to
* computeLineageSingleBinding. in this case the result map only contains
* one entry
- *
+ *
* @param workflowRun
* @param var
* @param proc
@@ -313,7 +291,7 @@ public class ProvenanceAnalysis {
* @throws SQLException
*/
public Map<String, List<Dependencies>> computeLineageSingleVar(
- String workflowRun, // dynamic scope
+ String workflowRun, // dynamic scope
String workflowId, // static scope
String var, // target var
String proc, // qualified with its processor name
@@ -364,7 +342,7 @@ public class ProvenanceAnalysis {
/**
* main lineage query method. queries the provenance DB with a single
* originating proc/var/path and a set of selected Processors
- *
+ *
* @param workflowRunId
* @param var
* @param proc
@@ -477,7 +455,7 @@ public class ProvenanceAnalysis {
/**
* accounts for an inverse transformation from one output to all inputs of a
* processor
- *
+ *
* @param workflowRunId
* @param var
* the output var
@@ -517,7 +495,7 @@ public class ProvenanceAnalysis {
if (getPq().isDataflow(proc)) { // if we are looking at the output of an entire dataflow
// force the "input vars" for this step to be the output var itself
- // this causes the following xfer step to trace back to the next processor _within_ proc
+ // this causes the following xfer step to trace back to the next processor _within_ proc
inputVars = new ArrayList<>();
inputVars.add(outputVar);
} else if (proc.equals(OUTPUT_CONTAINER_PROCESSOR)) { // same action as prev case, but may change in the future
@@ -558,13 +536,13 @@ public class ProvenanceAnalysis {
for (Port inputVar: inputVars)
var2Path.put(inputVar, null);
} else { // compute projected paths
- String[] projectedPath;
+ String[] projectedPath;
int start = 0;
for (Port inputVar: inputVars) {
// 24/7/08 get DNL (declared nesting level) and ANL (actual nesting level) from VAR
// TODO account for empty paths
- int projectedPathLength = var2delta.get(inputVar); // this is delta
+ int projectedPathLength = var2delta.get(inputVar); // this is delta
if (projectedPathLength == 0) {
// associate empty path to this var
@@ -589,7 +567,7 @@ public class ProvenanceAnalysis {
}
}
- // accumulate this proc to current path
+ // accumulate this proc to current path
currentPath.add(proc);
/*
@@ -617,7 +595,7 @@ public class ProvenanceAnalysis {
///////////
/// generate SQL if necessary -- for all input vars, based on the current path
- /// the projected paths are required to determine the level in the collection at which
+ /// the projected paths are required to determine the level in the collection at which
/// we look at the value assignment
///////////
@@ -686,7 +664,7 @@ public class ProvenanceAnalysis {
logger.debug("deref value for ref: " + ref + " "
+ data + " of class "
+ data.getClass().getName());
-
+
try {
aOPMManager.addArtifact(vb.getValue(), data);
} catch (ProvenanceException e) {
@@ -707,7 +685,7 @@ public class ProvenanceAnalysis {
/*
* assert proc as Process -- include iteration vector to
* separate different activations of the same process
- */
+ */
try {
aOPMManager.addProcess(proc, vb.getIteration(),
workflowId, vb.getWorkflowRunId());
@@ -731,7 +709,7 @@ public class ProvenanceAnalysis {
}
}
}
- //
+ //
// create OPM process for this xform
//
for (LineageSQLQuery lq : newLqList) {
@@ -808,7 +786,7 @@ public class ProvenanceAnalysis {
logger.warn("Could not add artifact", e);
}
- // true -> prevent duplicates CHECK
+ // true -> prevent duplicates CHECK
}
}
}
@@ -820,7 +798,7 @@ public class ProvenanceAnalysis {
xferStep(workflowRunId, workflowId, inputVar,
var2Path.get(inputVar), selectedProcessors, lqList);
}
- currentPath.remove(currentPath.size()-1); // CHECK
+ currentPath.remove(currentPath.size()-1); // CHECK
} // end xformStep
private void xferStep(String workflowRunId, String workflowId, Port port,
@@ -848,12 +826,12 @@ public class ProvenanceAnalysis {
// in this case set path to null
// retrieve full record for var:
- // retrieve input vars for current processor
+ // retrieve input vars for current processor
Map<String, String> varsQueryConstraints = new HashMap<>();
// varsQueryConstraints.put("W.workflowId", workflowRunId);
varsQueryConstraints.put("portId", a.getSourcePortId());
-// varsQueryConstraints.put("processorNameRef", sourceProcName);
+// varsQueryConstraints.put("processorNameRef", sourceProcName);
// varsQueryConstraints.put("portName", sourcePortName);
List<Port> varList = getPq().getPorts(varsQueryConstraints);
@@ -876,9 +854,9 @@ public class ProvenanceAnalysis {
private boolean isXform = true;
private String iteration = ""; // this is the iteration projected on a single variable. Used for propagation upwards default is no iteration --
- private String iterationVector = ""; // iteration vector accounts for cross-products. Used to be matched exactly in queries.
- private int iic = 0; // index in collection -- default is 0
- private int collectionNesting = 0; // n indicates granularity is n levels from leaf.
+ private String iterationVector = ""; // iteration vector accounts for cross-products. Used to be matched exactly in queries.
+ private int iic = 0; // index in collection -- default is 0
+ private int collectionNesting = 0; // n indicates granularity is n levels from leaf.
// This quantifies loss of lineage precision when working with collections
private String collectionRef = null;
private String proc;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceQuery.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceQuery.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceQuery.java
index 901120c..fe3918b 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceQuery.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceQuery.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import static org.apache.taverna.provenance.connector.AbstractProvenanceConnector.DataflowInvocationTable.DataflowInvocation;
import static org.apache.taverna.provenance.connector.AbstractProvenanceConnector.DataflowInvocationTable.parentProcessorEnactmentId;
@@ -767,7 +745,7 @@ public abstract class ProvenanceQuery {
* 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
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceWriter.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceWriter.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceWriter.java
index f52be6e..9419606 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceWriter.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/ProvenanceWriter.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import static org.apache.taverna.provenance.connector.AbstractProvenanceConnector.DataflowInvocationTable.DataflowInvocation;
@@ -71,11 +49,11 @@ import org.apache.taverna.configuration.database.DatabaseManager;
* Handles all the writing out of provenance items to the database layer. Uses
* standard SQL so all specific instances of this class can extend this writer
* to handle all of the db writes
- *
+ *
* @author Paolo Missier
* @author Ian Dunlop
* @author Stuart Owen
- *
+ *
*/
public class ProvenanceWriter {
@@ -99,7 +77,7 @@ public class ProvenanceWriter {
/**
* add each Port as a row into the Port DB table <strong>note: no static
* port type available as part of the dataflow...</strong>
- *
+ *
* @param ports
* @param wfId
* @throws SQLException
@@ -162,7 +140,7 @@ public class ProvenanceWriter {
/**
* inserts one row into the ARC DB table
- *
+ *
* @param sourcePort
* @param destinationPort
* @param workflowId
@@ -244,7 +222,7 @@ public class ProvenanceWriter {
/**
* insert new processor into the provenance DB
- *
+ *
* @param name
* @throws SQLException
*/
@@ -263,7 +241,7 @@ public class ProvenanceWriter {
/**
* add a processor to the static portion of the DB with given name, type and
* workflowId scope
- *
+ *
* @param name
* @param type
* @param workflowId
@@ -425,7 +403,7 @@ public class ProvenanceWriter {
/**
* persists var v back to DB
- *
+ *
* @param v
* @throws SQLException
*/
@@ -520,7 +498,7 @@ public class ProvenanceWriter {
/**
* deletes DB contents for the static structures -- called prior to each run
- *
+ *
* @throws SQLException
*/
public void clearDBStatic() throws SQLException {
@@ -539,7 +517,7 @@ public class ProvenanceWriter {
/**
* deletes DB contents for the static structures -- called prior to each run
- *
+ *
* @throws SQLException
*/
public void clearDBStatic(String wfID) throws SQLException {
@@ -594,7 +572,7 @@ public class ProvenanceWriter {
}
/**
* deletes DB contents for all runs -- for testing purposes
- *
+ *
* @throws SQLException
*/
public Set<String> clearDBDynamic(String runID) throws SQLException {
@@ -657,7 +635,7 @@ public class ProvenanceWriter {
/**
* used to support the implementation of
- *
+ *
* @param pname
* @param vFrom
* @param valFrom
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/URIGenerator.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/URIGenerator.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/URIGenerator.java
index f3d776c..90631ca 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/URIGenerator.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/URIGenerator.java
@@ -1,5 +1,3 @@
-package org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -8,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -18,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import java.net.URI;
import java.net.URISyntaxException;
@@ -28,7 +26,7 @@ public class URIGenerator {
public String makeT2ReferenceURI(String collId) {
// collId is of the form t2:list//<UUID>
// map to a proper URI
-
+
String[] tokens = collId.split("//");
String type = tokens[0].split(":")[1];
String namespace = tokens[1].split("/")[0].split("\\?")[0];
@@ -45,7 +43,7 @@ public class URIGenerator {
}
public String makePortURI(String wfId, String pName, String vName,
- boolean inputPort) {
+ boolean inputPort) {
return makeProcessorURI(pName, wfId) + (inputPort ? "in/" : "out/")
+ escape(vName);
}
@@ -58,7 +56,7 @@ public class URIGenerator {
throw new RuntimeException("Can't escape URI part " + part, e);
}
}
-
+
public String makeProcessorURI(String pName, String wfId) {
return makeWorkflowURI(wfId) + "processor/" + escape(pName) + "/";
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/WorkflowDataProcessor.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/WorkflowDataProcessor.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/WorkflowDataProcessor.java
index 0dac19e..0304364 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/WorkflowDataProcessor.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/WorkflowDataProcessor.java
@@ -1,8 +1,3 @@
-/**
- *
- */
-package org.apache.taverna.provenance.lineageservice;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -11,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -21,7 +16,7 @@ package org.apache.taverna.provenance.lineageservice;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice;
import static org.apache.taverna.provenance.lineageservice.utils.ProvenanceUtils.iterationToString;
import static org.apache.taverna.provenance.lineageservice.utils.ProvenanceUtils.parentProcess;
@@ -55,11 +50,11 @@ public class WorkflowDataProcessor {
private static Logger logger = Logger.getLogger(WorkflowDataProcessor.class);
// set of trees (impl as lists), one for each portName
- // PM portName not enough must use the WFID as context as well, because the same output portName
- // may occur in multiple nested workflows
- Map<String, List<WorkflowDataNode>> workflowDataTrees = new HashMap<>();
+ // PM portName not enough must use the WFID as context as well, because the same output portName
+ // may occur in multiple nested workflows
+ Map<String, List<WorkflowDataNode>> workflowDataTrees = new HashMap<>();
- protected Map<String, Timestamp> workflowStarted = new ConcurrentHashMap<>();
+ protected Map<String, Timestamp> workflowStarted = new ConcurrentHashMap<>();
ProvenanceQuery pq=null;
ProvenanceWriter pw = null;
@@ -71,12 +66,12 @@ public class WorkflowDataProcessor {
* to the portName found in the item. Repeated invocations of this method
* incrementally reconstruct the tree structure for each of the workflow
* outputs
- *
+ *
* @param root
*/
public void addWorkflowDataItem(ProvenanceItem provenanceItem) {
WorkflowDataProvenanceItem workflowDataItem = (WorkflowDataProvenanceItem) provenanceItem;
-
+
WorkflowDataNode wdn = new WorkflowDataNode();
wdn.setProcessId(provenanceItem.getProcessId());
wdn.setPortName(workflowDataItem.getPortName());
@@ -113,7 +108,7 @@ public class WorkflowDataProcessor {
/**
* writes records to PortBinding or Collection by traversing the trees<br/>
* expect this to be invoked after workflow completion
- *
+ *
* @param workflowId
* the external name of the dataflow (not the UUID)
* @param workflowRunId
@@ -126,7 +121,7 @@ public class WorkflowDataProcessor {
// i:inputPortName -> t2Ref
Map<String, String> workflowPortData = new HashMap<>();
-
+
for (Map.Entry<String, List<WorkflowDataNode>> entry : workflowDataTrees
.entrySet()) {
String portName = entry.getKey();
@@ -148,7 +143,7 @@ public class WorkflowDataProcessor {
String portKey = (node.isInputPort() ? "/i:" : "/o:") + node.getPortName();
workflowPortData.put(portKey, node.getValue());
}
-
+
if (node.isList) {
logger.debug("creating collection entry for "
+ node.value + " with index " + node.index);
@@ -189,7 +184,7 @@ public class WorkflowDataProcessor {
vb.setPositionInColl(node.getRelativePosition());
} else
vb.setPositionInColl(1); // default
-
+
try {
getPw().addPortBinding(vb);
} catch (SQLException e) {
@@ -212,12 +207,12 @@ public class WorkflowDataProcessor {
List<Port> ports = getPq().getPortsForDataflow(workflowId);
String processId = completeEvent.getProcessId();
-
+
DataflowInvocation invocation = new DataflowInvocation();
invocation.setDataflowInvocationId(UUID.randomUUID().toString());
invocation.setWorkflowId(workflowId);
invocation.setWorkflowRunId(workflowRunId);
-
+
String parentProcessId = parentProcess(processId, 1);
if (parentProcessId != null) {
ProcessorEnactment procAct = invocationProcessToProcessEnactment
@@ -271,7 +266,7 @@ public class WorkflowDataProcessor {
/**
* @param node
- * @return the last digit in the index
+ * @return the last digit in the index
*/
private int getPosition(WorkflowDataNode node) {
String[] vector = node.getIndex()
@@ -299,8 +294,8 @@ public class WorkflowDataProcessor {
if (index11.equals("") && tokens2.length == 1)
return true;
- // [x1,x2, ...,xk] cannot be parent of [x1,x2,...xh] when k < h-1
- // because [x1,x2,...xh] is more than one level deeper than [x1,x2, ...,xk]
+ // [x1,x2, ...,xk] cannot be parent of [x1,x2,...xh] when k < h-1
+ // because [x1,x2,...xh] is more than one level deeper than [x1,x2, ...,xk]
if (tokens1.length != tokens2.length - 1)
return false;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/ActivityType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/ActivityType.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/ActivityType.java
index 5ccf871..56f2eef 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/ActivityType.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/ActivityType.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice.types;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice.types;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,14 +16,14 @@ package org.apache.taverna.provenance.lineageservice.types;
* specific language governing permissions and limitations
* under the License.
*/
-
+package org.apache.taverna.provenance.lineageservice.types;
import org.apache.taverna.provenance.lineageservice.types.ProvenanceEventType;
/**
- *
+ *
* @author Paolo Missier
- *
+ *
*/
public class ActivityType implements ProvenanceEventType {
private IterationType[] iteration;
@@ -62,7 +40,7 @@ public class ActivityType implements ProvenanceEventType {
/**
* Gets the iteration value for this ActivityType.
- *
+ *
* @return iteration
*/
public IterationType[] getIteration() {
@@ -71,7 +49,7 @@ public class ActivityType implements ProvenanceEventType {
/**
* Sets the iteration value for this ActivityType.
- *
+ *
* @param iteration
*/
public void setIteration(IterationType[] iteration) {
@@ -88,7 +66,7 @@ public class ActivityType implements ProvenanceEventType {
/**
* Gets the id value for this ActivityType.
- *
+ *
* @return id
*/
public java.lang.String getId() {
@@ -97,7 +75,7 @@ public class ActivityType implements ProvenanceEventType {
/**
* Sets the id value for this ActivityType.
- *
+ *
* @param id
*/
public void setId(java.lang.String id) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/7fc503c9/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/DataDocumentType.java
----------------------------------------------------------------------
diff --git a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/DataDocumentType.java b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/DataDocumentType.java
index f86a1fd..4681826 100644
--- a/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/DataDocumentType.java
+++ b/taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/DataDocumentType.java
@@ -1,25 +1,3 @@
-/*******************************************************************************
- * 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 org.apache.taverna.provenance.lineageservice.types;
-
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -28,9 +6,9 @@ package org.apache.taverna.provenance.lineageservice.types;
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@@ -38,12 +16,13 @@ package org.apache.taverna.provenance.lineageservice.types;
* specific language governing permissions and limitations
* under the License.
*/
+package org.apache.taverna.provenance.lineageservice.types;
/**
- *
+ *
* @author Paolo Missier
- *
+ *
*/
public class DataDocumentType implements ProvenanceEventType {
private String reference;
@@ -59,7 +38,7 @@ public class DataDocumentType implements ProvenanceEventType {
/**
* Gets the reference value for this DataDocumentType.
- *
+ *
* @return reference
*/
public String getReference() {
@@ -68,7 +47,7 @@ public class DataDocumentType implements ProvenanceEventType {
/**
* Sets the reference value for this DataDocumentType.
- *
+ *
* @param reference
*/
public void setReference(String reference) {
@@ -77,7 +56,7 @@ public class DataDocumentType implements ProvenanceEventType {
/**
* Gets the id value for this DataDocumentType.
- *
+ *
* @return id
*/
public String getId() {
@@ -86,7 +65,7 @@ public class DataDocumentType implements ProvenanceEventType {
/**
* Sets the id value for this DataDocumentType.
- *
+ *
* @param id
*/
public void setId(String id) {