Author: clopes
Date: 2012-10-23 09:40:59 -0700 (Tue, 23 Oct 2012)
New Revision: 30694
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
Log:
Fixes #1539 (ClassCastException when opening a Cy2 session that has nested
networks and discrete mappings for attribute "has_nested_network"):
It now always recreates the attribute "has_nested_network" as a Boolean-typed
column when loading sessions or importing XGMML files; the value "yes" is
converted to true.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java
2012-10-22 23:04:02 UTC (rev 30693)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java
2012-10-23 16:40:59 UTC (rev 30694)
@@ -69,9 +69,10 @@
}
public static boolean fromXGMMLBoolean(final String s) {
- // should be only "1", but let's be nice and also accept "true"
+ // Should be only "1", but let's be nice and also accept "true"
//
http://www.cs.rpi.edu/research/groups/pb/punin/public_html/XGMML/draft-xgmml-20001006.html#BT
- return s != null && s.matches("(?i)1|true");
+ // We also accept "yes", because of Cy2 "has_nested_network" attribute
+ return s != null && s.matches("(?i)1|true|yes");
}
public static String toXGMMLBoolean(final Boolean value) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2012-10-22 23:04:02 UTC (rev 30693)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2012-10-23 16:40:59 UTC (rev 30694)
@@ -172,7 +172,11 @@
ParseState parseState = ParseState.NONE;
final String name = atts.getValue("name");
- final String type = atts.getValue("type");
+ String type = atts.getValue("type");
+
+ if ("has_nested_network".equals(name))
+ type = ObjectType.BOOLEAN.getName();
+
final boolean isEquation =
ObjectTypeMap.fromXGMMLBoolean(atts.getValue("cy:equation"));
final boolean isHidden =
ObjectTypeMap.fromXGMMLBoolean(atts.getValue("cy:hidden"));
--
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