From 2b07331c18608888aaa36cab5ade4b4673b3a24f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 30 Jun 2017 13:54:12 +0200
Subject: [PATCH] reactome stable identifier changes

---
 .../model/ReactomeStableIdentifier.java       | 79 ++++++++++++++++++-
 .../DatabaseObjectColumnParser.java           |  4 +-
 .../StableIdentifierColumnParser.java         |  6 ++
 3 files changed, 83 insertions(+), 6 deletions(-)

diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeStableIdentifier.java b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeStableIdentifier.java
index aca56837f9..99ac1b80b6 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeStableIdentifier.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeStableIdentifier.java
@@ -9,17 +9,37 @@ package lcsb.mapviewer.reactome.model;
  * 
  */
 public class ReactomeStableIdentifier extends ReactomeDatabaseObject {
+
 	/**
-	 * Identifier in reactome model. More information can be found <a
-	 * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
+	 * Identifier in reactome model. More information can be found
+	 * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
 	 */
 	private String	identifier;
+
 	/**
-	 * Identifier version in reactome model. More information can be found <a
-	 * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
+	 * Identifier version in reactome model. More information can be found
+	 * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
 	 */
 	private String	identifierVersion;
 
+	/**
+	 * Old identifier used in reactome model. More information can be found
+	 * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
+	 */
+	private String	oldIdentifier;
+
+	/**
+	 * Old identifier version used in reactome model. More information can be
+	 * found
+	 * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
+	 */
+	private String	oldIdentifierVersion;
+
+	/**
+	 * Undocumented by reactome...
+	 */
+	private boolean	released;
+
 	/**
 	 * @return the identifier
 	 * @see #identifier
@@ -54,4 +74,55 @@ public class ReactomeStableIdentifier extends ReactomeDatabaseObject {
 		this.identifierVersion = identifierVersion;
 	}
 
+	/**
+	 * @return the oldIdentifier
+	 * @see #oldIdentifier
+	 */
+	public String getOldIdentifier() {
+		return oldIdentifier;
+	}
+
+	/**
+	 * @param oldIdentifier
+	 *          the oldIdentifier to set
+	 * @see #oldIdentifier
+	 */
+	public void setOldIdentifier(String oldIdentifier) {
+		this.oldIdentifier = oldIdentifier;
+	}
+
+	/**
+	 * @return the oldIdentifierVersion
+	 * @see #oldIdentifierVersion
+	 */
+	public String getOldIdentifierVersion() {
+		return oldIdentifierVersion;
+	}
+
+	/**
+	 * @param oldIdentifierVersion
+	 *          the oldIdentifierVersion to set
+	 * @see #oldIdentifierVersion
+	 */
+	public void setOldIdentifierVersion(String oldIdentifierVersion) {
+		this.oldIdentifierVersion = oldIdentifierVersion;
+	}
+
+	/**
+	 * @return the released
+	 * @see #released
+	 */
+	public boolean isReleased() {
+		return released;
+	}
+
+	/**
+	 * @param released
+	 *          the released to set
+	 * @see #released
+	 */
+	public void setReleased(boolean released) {
+		this.released = released;
+	}
+
 }
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/DatabaseObjectColumnParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/DatabaseObjectColumnParser.java
index 448733a71f..b4f6aa1d20 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/DatabaseObjectColumnParser.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/DatabaseObjectColumnParser.java
@@ -47,8 +47,8 @@ public class DatabaseObjectColumnParser extends ColumnParser<ReactomeDatabaseObj
 		} else if (node.getNodeName().equalsIgnoreCase("stableIdentifier")) {
 			object.setStableIdentifier(getSiParser().parseSimplifiedObject(node));
 		} else {
-			throw new InvalidArgumentException("Unknown node type for ReactomeDatabaseObject: " + node.getNodeName() + ". Object: " + object.getClass() + " ["
-					+ object.getDbId() + "]");
+			throw new InvalidArgumentException(
+					"Unknown node type for ReactomeDatabaseObject: " + node.getNodeName() + ". Object: " + object.getClass() + " [" + object.getDbId() + "]");
 		}
 	}
 }
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/StableIdentifierColumnParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/StableIdentifierColumnParser.java
index 1beb753c1d..90947ae36f 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/StableIdentifierColumnParser.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/StableIdentifierColumnParser.java
@@ -27,6 +27,12 @@ public class StableIdentifierColumnParser extends ColumnParser<ReactomeStableIde
 			object.setIdentifier(node.getTextContent());
 		} else if (node.getNodeName().equalsIgnoreCase("identifierVersion")) {
 			object.setIdentifierVersion(node.getTextContent());
+		} else if (node.getNodeName().equalsIgnoreCase("oldIdentifier")) {
+			object.setOldIdentifier(node.getTextContent());
+		} else if (node.getNodeName().equalsIgnoreCase("oldIdentifierVersion")) {
+			object.setOldIdentifierVersion(node.getTextContent());
+		} else if (node.getNodeName().equalsIgnoreCase("released")) {
+			object.setReleased("true".equalsIgnoreCase(node.getTextContent()));
 		} else {
 			getParentParser().updateColumnFromNode(object, node);
 		}
-- 
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