Author: clopes
Date: 2012-08-13 09:06:58 -0700 (Mon, 13 Aug 2012)
New Revision: 30171
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/vizmap/VisualStyleSerializer.java
Log:
Catching exceptions when serializing visual properties/dependencies, so the
session can still be saved, even if one or more properties can't be serialized.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/vizmap/VisualStyleSerializer.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/vizmap/VisualStyleSerializer.java
2012-08-12 10:13:12 UTC (rev 30170)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/vizmap/VisualStyleSerializer.java
2012-08-13 16:06:58 UTC (rev 30171)
@@ -115,7 +115,7 @@
* @param styles The collection of VisualStyles that you wish to
convert into a serializable object.
* @return A Vizmap object that contains a representation of the
collection of visual styles.
*/
- public Vizmap createVizmap(Collection<VisualStyle> styles) {
+ public Vizmap createVizmap(final Collection<VisualStyle> styles) {
Vizmap vizmap = new Vizmap();
lexicon = renderingEngineManager.getDefaultVisualLexicon();
@@ -135,7 +135,7 @@
createVizmapProperties(vs,
BasicVisualLexicon.EDGE, vsModel.getEdge().getVisualProperty());
// Create Dependencies
- createDependency(vs, vsModel);
+ createDependencies(vs, vsModel);
}
}
@@ -183,7 +183,7 @@
createVisualProperties(vs,
CyEdge.class, vsModel.getEdge().getVisualProperty());
// Restore dependency
- restoreDependency(vs, vsModel);
+ restoreDependencies(vs, vsModel);
// Do not add the modified default style to the
list!
if (!vs.equals(defStyle))
@@ -200,7 +200,7 @@
* @param vizmap A Properties object containing a representation of
VisualStyles.
* @return A collection of VisualStyle objects.
*/
- public Set<VisualStyle> createVisualStyles(Properties props) {
+ public Set<VisualStyle> createVisualStyles(final Properties props) {
// Convert properties to Vizmap:
Vizmap vizmap = new Vizmap();
List<org.cytoscape.io.internal.util.vizmap.model.VisualStyle>
vizmapStyles = vizmap.getVisualStyle();
@@ -256,103 +256,105 @@
return createVisualStyles(vizmap);
}
- @SuppressWarnings("unchecked")
- private void createVizmapProperties(VisualStyle vs,
VisualProperty<Visualizable> root,
-
List<org.cytoscape.io.internal.util.vizmap.model.VisualProperty> vpModelList) {
+ @SuppressWarnings({ "unchecked", "rawtypes" })
+ private void createVizmapProperties(final VisualStyle vs, final
VisualProperty<Visualizable> root,
+ final
List<org.cytoscape.io.internal.util.vizmap.model.VisualProperty> vpModelList) {
final Collection<VisualProperty<?>> vpList =
lexicon.getAllDescendants(root);
final Iterator<VisualProperty<?>> iter = vpList.iterator();
while (iter.hasNext()) {
- final VisualProperty<Object> vp =
(VisualProperty<Object>) iter.next();
-
- // NETWORK root includes NODES and EDGES, but we want
to separate the CyNetwork properties!
- if (root == BasicVisualLexicon.NETWORK &&
vp.getTargetDataType() != CyNetwork.class) continue;
-
- Object defValue = vs.getDefaultValue(vp);
- final VisualMappingFunction<?, ?> mapping =
vs.getVisualMappingFunction(vp);
-
- if (defValue != null || mapping != null) {
-
org.cytoscape.io.internal.util.vizmap.model.VisualProperty vpModel = new
org.cytoscape.io.internal.util.vizmap.model.VisualProperty();
- vpModel.setName(vp.getIdString());
-
- vpModelList.add(vpModel);
-
- if (defValue != null) {
- String sValue = null;
-
- sValue =
vp.toSerializableString(defValue);
-
- if (sValue != null)
- vpModel.setDefault(sValue);
- }
-
- if (mapping instanceof PassthroughMapping<?,
?>) {
- PassthroughMapping<?, ?> pm =
(PassthroughMapping<?, ?>) mapping;
- AttributeType attrType =
toAttributeType(pm.getMappingColumnType());
-
-
org.cytoscape.io.internal.util.vizmap.model.PassthroughMapping pmModel = new
org.cytoscape.io.internal.util.vizmap.model.PassthroughMapping();
-
pmModel.setAttributeName(pm.getMappingColumnName());
- pmModel.setAttributeType(attrType);
-
- vpModel.setPassthroughMapping(pmModel);
-
- } else if (mapping instanceof
DiscreteMapping<?, ?>) {
- DiscreteMapping<?, ?> dm =
(DiscreteMapping<?, ?>) mapping;
- AttributeType attrType =
toAttributeType(dm.getMappingColumnType());
-
-
org.cytoscape.io.internal.util.vizmap.model.DiscreteMapping dmModel = new
org.cytoscape.io.internal.util.vizmap.model.DiscreteMapping();
-
dmModel.setAttributeName(dm.getMappingColumnName());
- dmModel.setAttributeType(attrType);
-
- Map<?, ?> map = dm.getAll();
-
- for (Map.Entry<?, ?> entry :
map.entrySet()) {
- DiscreteMappingEntry entryModel
= new DiscreteMappingEntry();
-
entryModel.setAttributeValue(entry.getKey().toString());
-
entryModel.setValue(vp.toSerializableString(entry.getValue()));
-
-
dmModel.getDiscreteMappingEntry().add(entryModel);
- }
-
- vpModel.setDiscreteMapping(dmModel);
-
- } else if (mapping instanceof
ContinuousMapping<?, ?>) {
- final ContinuousMapping<?,?> cm =
(ContinuousMapping<?, ?>) mapping;
- AttributeType attrType =
toAttributeType(cm.getMappingColumnType());
-
-
org.cytoscape.io.internal.util.vizmap.model.ContinuousMapping cmModel = new
org.cytoscape.io.internal.util.vizmap.model.ContinuousMapping();
-
cmModel.setAttributeName(cm.getMappingColumnName());
- cmModel.setAttributeType(attrType);
-
- List<?> points = cm.getAllPoints();
-
- for (Object point : points) {
- ContinuousMappingPoint<?, ?>
continuousPoint = (ContinuousMappingPoint<?, ?>) point;
-
org.cytoscape.io.internal.util.vizmap.model.ContinuousMappingPoint pModel = new
org.cytoscape.io.internal.util.vizmap.model.ContinuousMappingPoint();
-
- Object originalValue =
continuousPoint.getValue();
+ final VisualProperty vp = iter.next();
+
+ try {
+ // NETWORK root includes NODES and EDGES, but
we want to separate the CyNetwork properties!
+ if (root == BasicVisualLexicon.NETWORK &&
vp.getTargetDataType() != CyNetwork.class)
+ continue;
+
+ Object defValue = vs.getDefaultValue(vp);
+ final VisualMappingFunction<?, ?> mapping =
vs.getVisualMappingFunction(vp);
+
+ if (defValue != null || mapping != null) {
+
org.cytoscape.io.internal.util.vizmap.model.VisualProperty vpModel = new
org.cytoscape.io.internal.util.vizmap.model.VisualProperty();
+ vpModel.setName(vp.getIdString());
+
+ vpModelList.add(vpModel);
+
+ if (defValue != null) {
+ String sValue = null;
- final String sValue =
originalValue.toString();
- final BigDecimal value = new
BigDecimal(sValue);
- pModel.setAttrValue(value);
+ sValue =
vp.toSerializableString(defValue);
- Object lesser =
continuousPoint.getRange().lesserValue;
- Object equal =
continuousPoint.getRange().equalValue;
- Object greater =
continuousPoint.getRange().greaterValue;
-
-//
System.out.println(cm.getVisualProperty().getDisplayName() + ": ***Point is "
-// +
lesser.getClass() + ", " + equal.getClass() +", " + greater.getClass());
-
-
pModel.setLesserValue(vp.toSerializableString(lesser));
-
pModel.setEqualValue(vp.toSerializableString(equal));
-
pModel.setGreaterValue(vp.toSerializableString(greater));
-
-
cmModel.getContinuousMappingPoint().add(pModel);
+ if (sValue != null)
+
vpModel.setDefault(sValue);
}
-
- vpModel.setContinuousMapping(cmModel);
+
+ if (mapping instanceof
PassthroughMapping<?, ?>) {
+ PassthroughMapping<?, ?> pm =
(PassthroughMapping<?, ?>) mapping;
+ AttributeType attrType =
toAttributeType(pm.getMappingColumnType());
+
+
org.cytoscape.io.internal.util.vizmap.model.PassthroughMapping pmModel = new
org.cytoscape.io.internal.util.vizmap.model.PassthroughMapping();
+
pmModel.setAttributeName(pm.getMappingColumnName());
+
pmModel.setAttributeType(attrType);
+
+
vpModel.setPassthroughMapping(pmModel);
+
+ } else if (mapping instanceof
DiscreteMapping<?, ?>) {
+ DiscreteMapping<?, ?> dm =
(DiscreteMapping<?, ?>) mapping;
+ AttributeType attrType =
toAttributeType(dm.getMappingColumnType());
+
+
org.cytoscape.io.internal.util.vizmap.model.DiscreteMapping dmModel = new
org.cytoscape.io.internal.util.vizmap.model.DiscreteMapping();
+
dmModel.setAttributeName(dm.getMappingColumnName());
+
dmModel.setAttributeType(attrType);
+
+ Map<?, ?> map = dm.getAll();
+
+ for (Map.Entry<?, ?> entry :
map.entrySet()) {
+ DiscreteMappingEntry
entryModel = new DiscreteMappingEntry();
+
entryModel.setAttributeValue(entry.getKey().toString());
+
entryModel.setValue(vp.toSerializableString(entry.getValue()));
+
+
dmModel.getDiscreteMappingEntry().add(entryModel);
+ }
+
+
vpModel.setDiscreteMapping(dmModel);
+
+ } else if (mapping instanceof
ContinuousMapping<?, ?>) {
+ final ContinuousMapping<?,?> cm
= (ContinuousMapping<?, ?>) mapping;
+ AttributeType attrType =
toAttributeType(cm.getMappingColumnType());
+
+
org.cytoscape.io.internal.util.vizmap.model.ContinuousMapping cmModel = new
org.cytoscape.io.internal.util.vizmap.model.ContinuousMapping();
+
cmModel.setAttributeName(cm.getMappingColumnName());
+
cmModel.setAttributeType(attrType);
+
+ List<?> points =
cm.getAllPoints();
+
+ for (Object point : points) {
+
ContinuousMappingPoint<?, ?> continuousPoint = (ContinuousMappingPoint<?, ?>)
point;
+
org.cytoscape.io.internal.util.vizmap.model.ContinuousMappingPoint pModel = new
org.cytoscape.io.internal.util.vizmap.model.ContinuousMappingPoint();
+
+ Object originalValue =
continuousPoint.getValue();
+
+ final String sValue =
originalValue.toString();
+ final BigDecimal value
= new BigDecimal(sValue);
+
pModel.setAttrValue(value);
+
+ Object lesser =
continuousPoint.getRange().lesserValue;
+ Object equal =
continuousPoint.getRange().equalValue;
+ Object greater =
continuousPoint.getRange().greaterValue;
+
+
pModel.setLesserValue(vp.toSerializableString(lesser));
+
pModel.setEqualValue(vp.toSerializableString(equal));
+
pModel.setGreaterValue(vp.toSerializableString(greater));
+
+
cmModel.getContinuousMappingPoint().add(pModel);
+ }
+
+
vpModel.setContinuousMapping(cmModel);
+ }
}
+ } catch (final Exception e) {
+ logger.error("Cannot save visual property: " +
(vp != null ? vp.getDisplayName() : ""), e);
}
}
}
@@ -500,7 +502,7 @@
}
}
- private void createDependency(final VisualStyle visualStyle,
+ private void createDependencies(final VisualStyle visualStyle,
org.cytoscape.io.internal.util.vizmap.model.VisualStyle
vsModel) {
// Create serializable Dependency
final Set<VisualPropertyDependency<?>> dependencies =
visualStyle.getAllVisualPropertyDependencies();
@@ -511,25 +513,28 @@
Collection<VisualProperty<?>> nodeVisualProperties =
lexicon.getAllDescendants(BasicVisualLexicon.NODE);
Collection<VisualProperty<?>> edgeVisualProperties =
lexicon.getAllDescendants(BasicVisualLexicon.EDGE);
- Collection<VisualProperty<?>> networkVisualProperties =
lexicon.getAllDescendants(BasicVisualLexicon.NETWORK);
for (VisualPropertyDependency<?> vpDep : dependencies) {
- final Dependency newDependency = new Dependency();
- newDependency.setName(vpDep.getIdString());
- newDependency.setValue(vpDep.isDependencyEnabled());
-
- final VisualProperty<?> parent =
vpDep.getParentVisualProperty();
-
- if (nodeVisualProperties.contains(parent))
- nodeDep.add(newDependency);
- else if (edgeVisualProperties.contains(parent))
- edgeDep.add(newDependency);
- else
- networkDep.add(newDependency);
+ try {
+ final Dependency newDependency = new
Dependency();
+ newDependency.setName(vpDep.getIdString());
+
newDependency.setValue(vpDep.isDependencyEnabled());
+
+ final VisualProperty<?> parent =
vpDep.getParentVisualProperty();
+
+ if (nodeVisualProperties.contains(parent))
+ nodeDep.add(newDependency);
+ else if (edgeVisualProperties.contains(parent))
+ edgeDep.add(newDependency);
+ else
+ networkDep.add(newDependency);
+ } catch (final Exception e) {
+ logger.error("Cannot save dependency: " +
(vpDep != null ? vpDep.getDisplayName() : ""), e);
+ }
}
}
- private void restoreDependency(final VisualStyle visualStyle,
org.cytoscape.io.internal.util.vizmap.model.VisualStyle vsModel) {
+ private void restoreDependencies(final VisualStyle visualStyle,
org.cytoscape.io.internal.util.vizmap.model.VisualStyle vsModel) {
final Node nodeSection = vsModel.getNode();
final Edge edgeSection = vsModel.getEdge();
final Network networkSection = vsModel.getNetwork();
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