Author: Christian Lopes
Date: 2011-01-04 16:11:24 -0800 (Tue, 04 Jan 2011)
New Revision: 23297
Added:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/error/
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/error/CWError.as
Modified:
cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test1.graphml
cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test2.xgmml
cytoscapeweb/trunk/cytoscapeweb/html-template/js/tests.js
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/ExternalObjectConverterTest.as
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/XGMMLConverterTest.as
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/view/render/ImageCacheTest.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/AddDataFieldCommand.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/DrawGraphCommand.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/ExportNetworkCommand.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/RemoveItemsCommand.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/UpdateDataCommand.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/GraphProxy.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/ExternalObjectConverter.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/XGMMLConverter.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/methods/error.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/util/ErrorCodes.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/ExternalMediator.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/render/ImageCache.as
Log:
Improved error handling to add codes.
XGMML now accepts both "0"|"1" and "true"|"false" as boolean types.
CW now throws errors when trying to draw/update a network with invalid data
values (node/edge ID has to be a string from now on).
Fixed bugs:
- #2447: Date attributes exported as null to XGMML
- #2445: Wrong data field types when using JavaScript objects as the
network data
- #2444: Null "number" values converted to 0 when updating data
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test1.graphml
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test1.graphml
2011-01-04 20:59:57 UTC (rev 23296)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test1.graphml
2011-01-05 00:11:24 UTC (rev 23297)
@@ -1,8 +1,10 @@
<graphml>
<key id="weight" for="node" attr.name="weight" attr.type="double"/>
+ <key id="ranking" for="node" attr.name="ranking" attr.type="int"/>
<key id="type" for="node" attr.name="type" attr.type="string"/>
<key id="shape" for="node" attr.name="shape" attr.type="string"/>
<key id="label" for="node" attr.name="label" attr.type="string"/>
+ <key id="special" for="node" attr.name="special" attr.type="boolean"/>
<key id="type" for="edge" attr.name="type" attr.type="string"/>
<key id="interaction" for="edge" attr.name="interaction" attr.type="string">
@@ -15,33 +17,43 @@
<graph edgedefault="undirected">
<node id="1">
<data key="weight">0.45</data>
+ <data key="ranking">1</data>
<data key="label">n1</data>
<data key="type">1</data>
<data key="shape">ELLIPSE</data>
+ <data key="special">false</data>
</node>
<node id="2">
<data key="weight">0.22</data>
+ <data key="ranking">2</data>
<data key="label">n2</data>
<data key="type">2</data>
<data key="shape">TRIANGLE</data>
+ <data key="special">true</data>
</node>
<node id="3">
<data key="weight">0.09</data>
+ <data key="ranking">3</data>
<data key="label">n3</data>
<data key="type">1</data>
<data key="shape">OCTAGON</data>
+ <data key="special">false</data>
</node>
<node id="4">
<data key="weight">0.03</data>
+ <data key="ranking">4</data>
<data key="label">n4</data>
<data key="type">1</data>
<data key="shape">DIAMOND</data>
+ <data key="special">false</data>
</node>
<node id="5">
<data key="weight">0.10</data>
+ <data key="ranking">5</data>
<data key="label">n5</data>
<data key="type">3</data>
<data key="shape">PARALLELOGRAM</data>
+ <data key="special">false</data>
</node>
<edge target="1" source="2" directed="true">
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test2.xgmml
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test2.xgmml
2011-01-04 20:59:57 UTC (rev 23296)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test2.xgmml
2011-01-05 00:11:24 UTC (rev 23297)
@@ -4,31 +4,43 @@
<att type="real" name="GRAPH_VIEW_ZOOM" value="1"/>
<att type="real" name="GRAPH_VIEW_CENTER_X" value="0"/>
<att type="real" name="GRAPH_VIEW_CENTER_Y" value="0"/>
+
<node id="101" weight="0.45" label="A01">
<att type="string" name="type" value="1"/>
+ <att type="integer" name="ranking" value="1"/>
<att type="string" name="shape" value="ELLIPSE"/>
+ <att type="boolean" name="special" value="1"/>
<graphics x="387.25" y="304" fill="#cccccc" outline="#333333" w="36"
cy:nodeTransparency="0.8" cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE"
h="36" width="1"/>
</node>
<node id="102" weight="0.22" label="A02">
<att type="string" name="type" value="2"/>
+ <att type="integer" name="ranking" value="2"/>
<att type="string" name="shape" value="TRIANGLE"/>
+ <att type="boolean" name="special" value="0"/>
<graphics x="324.85" y="340" fill="#cccccc" outline="#333333"
w="22.857142857142854" cy:nodeTransparency="0.8"
cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE" h="22.857142857142854"
width="1"/>
</node>
<node id="103" weight="0.09" label="A03">
<att type="string" name="type" value="2"/>
+ <att type="integer" name="ranking" value="3"/>
<att type="string" name="shape" value="OCTAGON"/>
+ <att type="boolean" name="special" value="0"/>
<graphics x="324.85" y="412" fill="#cccccc" outline="#333333"
w="15.428571428571429" cy:nodeTransparency="0.8"
cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE" h="15.428571428571429"
width="1"/>
</node>
<node id="104" weight="0.03" label="A04">
<att type="string" name="type" value="1"/>
+ <att type="integer" name="ranking" value="4"/>
<att type="string" name="shape" value="DIAMOND"/>
+ <att type="boolean" name="special" value="0"/>
<graphics x="387.25" y="448" fill="#cccccc" outline="#333333" w="12"
cy:nodeTransparency="0.8" cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE"
h="12" width="1"/>
</node>
<node id="105" weight="0.1" label="A05">
<att type="string" name="type" value="3"/>
+ <att type="integer" name="ranking" value="5"/>
<att type="string" name="shape" value="PARALLELOGRAM"/>
+ <att type="boolean" name="special" value="0"/>
<graphics x="449.6" y="339.95" fill="#cccccc" outline="#333333" w="16"
cy:nodeTransparency="0.8" cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE"
h="16" width="1"/>
</node>
+
<edge id="1" target="101" source="102" weight="0.4" label="101 (25) 102">
<att type="string" name="directed" value="true"/>
<att type="string" name="sourceArrowShape" value="diamond"/>
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/js/tests.js
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/js/tests.js 2011-01-04
20:59:57 UTC (rev 23296)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/js/tests.js 2011-01-05
00:11:24 UTC (rev 23297)
@@ -998,13 +998,13 @@
var ids = [];
// 1: Update all nodes and edges (same data):
- var data = { weight: 1, new_attr: "ignore it!" };
+ var data = { weight: 1/*, new_attr: "ignore it!"*/ };
vis.updateData(data);
all = vis.nodes().concat(vis.edges());
$.each(all, function(i, el) {
same(el.data.weight, 1, "weight updated ("+el.data.id+")");
- same(el.data.new_attr, undefined, "New attribute ignored
("+el.data.id+")");
+// same(el.data.new_attr, undefined, "New attribute ignored
("+el.data.id+")");
});
// 2: Update more than one node and edge at once (by ID - ALL groups -
same data):
@@ -1086,6 +1086,31 @@
ok(el.data.label != n.data.label, "Other nodes or edges
label NOT updated ("+id+")");
}
});
+
+ var id = nodes[0].data.id;
+
+ // 6: Update a field with type 'number' to null (should work):
+ vis.updateData("nodes", [id], { weight: null });
+ ok(vis.node(id).data.weight === null, "Node weight should be null");
+
+ // Test Errors:
+ var errId;
+ var onError = function(evt) {console.log(evt.value.id);
+ errId = evt.value.id;
+ }
+ vis.addListener("error", onError);
+
+ // 7: Update a field with type 'int' to null (should set 0 as default):
+ vis.updateData("nodes", [id], { ranking: null });
+ same(errId, "dat001", "node.data.ranking (error: int type with null
value)");
+ errId = null;
+
+ // 8: Update a field with type 'boolean' to null (should set false as
default):
+ vis.updateData("nodes", [id], { special: null });
+ same(errId, "dat001", "node.data.special (error: boolean type with
null value)");
+ errId = null;
+
+ vis.removeListener("error", onError);
});
test("Get Data Schema", function() {
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/AddDataFieldCommand.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/AddDataFieldCommand.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/AddDataFieldCommand.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -31,6 +31,7 @@
import flare.data.DataUtil;
import org.cytoscapeweb.ApplicationFacade;
+ import org.cytoscapeweb.model.error.CWError;
import org.cytoscapeweb.model.methods.error;
import org.cytoscapeweb.util.Groups;
import org.puremvc.as3.interfaces.INotification;
@@ -68,7 +69,7 @@
if (added)
sendNotification(ApplicationFacade.GRAPH_DATA_CHANGED);
} catch (err:Error) {
trace("[ERROR]: AddDataFieldCommand.execute: " +
err.getStackTrace());
- error(err.message, err.errorID, err.name, err.getStackTrace());
+ error(err);
}
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/DrawGraphCommand.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/DrawGraphCommand.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/DrawGraphCommand.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -29,9 +29,8 @@
*/
package org.cytoscapeweb.controller {
- import flash.utils.setTimeout;
-
import org.cytoscapeweb.model.data.VisualStyleVO;
+ import org.cytoscapeweb.model.error.CWError;
import org.cytoscapeweb.model.methods.error;
import org.cytoscapeweb.view.GraphMediator;
import org.cytoscapeweb.view.components.GraphView;
@@ -84,10 +83,9 @@
graphMediator.drawGraph();
}
-
} catch (err:Error) {
trace("[ERROR]: DrawGraphCommand.execute: " +
err.getStackTrace());
- error(err.message, err.errorID, err.name, err.getStackTrace());
+ error(err);
}
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/ExportNetworkCommand.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/ExportNetworkCommand.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/ExportNetworkCommand.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -62,7 +62,7 @@
graphProxy.export(data, url, window);
} catch (err:Error) {
- error(err.message, err.errorID, err.name, err.getStackTrace());
+ error(err);
}
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/RemoveItemsCommand.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/RemoveItemsCommand.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/RemoveItemsCommand.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -64,7 +64,7 @@
} catch (err:Error) {
trace("[ERROR]: RemoveItemsCommand.execute: " +
err.getStackTrace());
- error(err.message, err.errorID, err.name, err.getStackTrace());
+ error(err);
}
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/UpdateDataCommand.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/UpdateDataCommand.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/controller/UpdateDataCommand.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -69,7 +69,7 @@
sendNotification(ApplicationFacade.GRAPH_DATA_CHANGED);
} catch (err:Error) {
trace("[ERROR]: UpdateDataCommand.execute: " +
err.getStackTrace());
- error(err.message, err.errorID, err.name, err.getStackTrace());
+ error(err);
}
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/GraphProxy.as
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/GraphProxy.as
2011-01-04 20:59:57 UTC (rev 23296)
+++ cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/GraphProxy.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -48,8 +48,8 @@
import mx.utils.StringUtil;
import org.cytoscapeweb.ApplicationFacade;
- import org.cytoscapeweb.model.converters.GraphMLConverter;
import org.cytoscapeweb.model.converters.ExternalObjectConverter;
+ import org.cytoscapeweb.model.converters.GraphMLConverter;
import org.cytoscapeweb.model.converters.SIFConverter;
import org.cytoscapeweb.model.converters.XGMMLConverter;
import org.cytoscapeweb.model.data.ConfigVO;
@@ -421,12 +421,10 @@
var f:DataField = schema.getFieldByName(k);
if (f != null) {
var v:* = data[k];
- v = DataUtil.parseValue(v, f.type);
-
- if (isNaN(v) && (f.type === DataUtil.INT || f.type
=== DataUtil.NUMBER))
- throw new Error("Attempt to convert
'"+data[k]+"' to NUMBER while updating the '"+k+"' data field");
-
+ v = ExternalObjectConverter.normalizeDataValue(v,
f.type, f.defaultValue);
ds.data[k] = v;
+ } else {
+ throw new Error("Cannot update data: there is no
Data Field for '"+k+".");
}
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/ExternalObjectConverter.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/ExternalObjectConverter.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/ExternalObjectConverter.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -44,6 +44,8 @@
import flash.utils.IDataInput;
import flash.utils.IDataOutput;
+ import org.cytoscapeweb.model.error.CWError;
+ import org.cytoscapeweb.util.ErrorCodes;
import org.cytoscapeweb.util.Groups;
import org.cytoscapeweb.util.Utils;
@@ -111,7 +113,7 @@
var nodes:Array = [], edges:Array = [];
var id:String, sid:String, tid:String;
var obj:Object;
- var f:DataField;
+ var f:DataField, type:int, defValue:*, mandatoryDefValue:*;
var directed:Boolean = false;
if (network == null) network = {};
@@ -140,7 +142,18 @@
} else {
f = schema.getFieldByName(name);
if (f == null) {
- schema.addField(new DataField(name, obj[TYPE],
obj[DEF_VALUE], name));
+ type = toCW_Type(obj[TYPE]);
+
+ // Some types always require a default value,
because they don't accept null.
+ switch(type) {
+ case DataUtil.INT: mandatoryDefValue = 0;
break;
+ case DataUtil.BOOLEAN: mandatoryDefValue =
false; break;
+ default: mandatoryDefValue = null;
+ }
+
+ defValue = normalizeDataValue(obj[DEF_VALUE],
type, mandatoryDefValue);
+
+ schema.addField(new DataField(name, type,
defValue, name));
}
}
}
@@ -157,24 +170,24 @@
// Nodes
for each (obj in extNodesData) {
- id = "" + obj[ID]; // always convert IDs to String!
normalizeData(obj, nodeSchema)
+ id = obj[ID];
lookup[id] = obj;
nodes.push(obj);
}
// Edges
for each (obj in extEdgesData) {
- id = "" + obj[ID];
- sid = "" + obj[SOURCE];
- tid = "" + obj[TARGET];
+ normalizeData(obj, edgeSchema);
+ id = obj[ID];
+ sid = obj[SOURCE];
+ tid = obj[TARGET];
if (!lookup.hasOwnProperty(sid))
throw new Error("Edge "+id+" references unknown node:
"+sid);
if (!lookup.hasOwnProperty(tid))
throw new Error("Edge "+id+" references unknown node:
"+tid);
-
- normalizeData(obj, edgeSchema)
+
edges.push(obj);
}
@@ -285,9 +298,7 @@
return obj;
}
- // ========[ PRIVATE METHODS
]==============================================================
-
- private static function normalizeData(data:Object,
schema:DataSchema):void {
+ public static function normalizeData(data:Object,
schema:DataSchema):void {
var name:String, field:DataField, value:*;
// Set default values, if necessary:
@@ -295,7 +306,7 @@
field = schema.getFieldAt(i);
name = field.name;
value = data[name];
- if (value === undefined) data[name] = field.defaultValue;
+ data[name] = normalizeDataValue(value, field.type,
field.defaultValue);
}
// Look for missing fields:
@@ -307,6 +318,36 @@
}
}
+ public static function normalizeDataValue(value:*, type:int,
defValue:*=undefined):* {
+ // Set default value, if necessary:
+ if (value === undefined) value = defValue !== undefined ? defValue
: null;
+
+ // Validate and normalize numeric values:
+ if (type === DataUtil.INT) {
+ if (value == null || isNaN(value))
+ throw new CWError("Invalid data type ("+(typeof value)+")
for field of type 'int': " + value,
+ ErrorCodes.INVALID_DATA_CONVERSION);
+ } else if (type === DataUtil.NUMBER) {
+ if (value === undefined) value = null;
+
+ if (value != null && isNaN(value))
+ throw new CWError("Invalid data type ("+(typeof value)+")
for field of type 'number': " + value,
+ ErrorCodes.INVALID_DATA_CONVERSION);
+ } else if (type === DataUtil.BOOLEAN) {
+ if (! (value is Boolean))
+ throw new CWError("Invalid data type ("+(typeof value)+")
for field of type 'boolean': " + value,
+ ErrorCodes.INVALID_DATA_CONVERSION);
+ } else if (type === DataUtil.STRING) {
+ if (value != null && !(value is String))
+ throw new CWError("Invalid data type ("+(typeof value)+")
for field of type 'string': " + value,
+ ErrorCodes.INVALID_DATA_CONVERSION);
+ }
+
+ return value
+ }
+
+ // ========[ PRIVATE METHODS
]==============================================================
+
// -- static helpers --------------------------------------------------
private static function toCW_Type(type:String):int {
@@ -326,8 +367,8 @@
case DataUtil.INT: return INT;
case DataUtil.BOOLEAN: return BOOLEAN;
case DataUtil.NUMBER: return NUMBER;
+ case DataUtil.STRING: return STRING;
case DataUtil.DATE:
- case DataUtil.STRING: return STRING;
case DataUtil.OBJECT:
default: return OBJECT;
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/XGMMLConverter.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/XGMMLConverter.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/XGMMLConverter.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -409,7 +409,7 @@
name = attribute.name().toString();
field = schema.getFieldByName(name);
if (field != null)
- data[name] = DataUtil.parseValue(attribute[0].toString(),
field.type);
+ data[name] = parseAttValue(attribute[0].toString(),
field.type);
}
// get "att" tags:
@@ -446,14 +446,14 @@
parseAtt(innerAtt, schema, innerData);
} else {
var innerType:int =
toCW_Type(innera...@[type].tostring());
- innerData = DataUtil.parseValue(innera...@[value],
innerType);
+ innerData = parseAttValue(innera...@[value],
innerType);
}
arr.push(innerData);
}
data[name] = arr;
} else {
// Otherwise, just add the single att data:
- data[name] = DataUtil.parseValue(a...@[value], type);
+ data[name] = parseAttValue(a...@[value], type);
}
}
@@ -570,14 +570,14 @@
private function addAtt(xml:XML, name:String, schema:DataSchema,
value:*):void {
var field:DataField = schema.getFieldByName(name);
var dataType:int = field != null ? field.type :
Utils.dataType(value);
- var type:String = fromCW_Type(dataType); // XGMML type
+ var type:String = fromCW_Type(dataType, value); // XGMML type
var att:XML = <{ATTRIBUTE}/>;
a...@[type] = type;
if (name != null) a...@[name] = name;
// Add <att> tags data:
- if (typeof value === "object") {
+ if (typeof value === "object" && !(value is Date)) {
// If it is an object or array, the att value is a list of
other att tags:
for (var k:String in value) {
var entryValue:* = value[k];
@@ -655,14 +655,28 @@
vp.vizMapper = dm;
}
- value = parseValue(propName, value);
+ value = parseGraphicsValue(propName, value);
dm.addEntry(id, value);
}
}
// -- static helpers --------------------------------------------------
- internal static function parseValue(propName:String, value:*):* {
+ internal static function parseAttValue(value:String, type:int):* {
+ var val:*;
+
+ if (type === DataUtil.BOOLEAN) {
+ // XGMML's boolean type is 0 or 1, but Cytoscape uses
true/false, so let's
+ // accept both:
+ val = value != null && (value === TRUE || value.toLowerCase()
=== "true");
+ } else {
+ val = DataUtil.parseValue(value, type);
+ }
+
+ return val;
+ }
+
+ internal static function parseGraphicsValue(propName:String,
value:*):* {
if (value != null) {
switch (propName) {
case VisualProperties.EDGE_SOURCE_ARROW_SHAPE:
@@ -713,6 +727,7 @@
switch (type) {
case INTEGER: return DataUtil.INT;
case REAL: return DataUtil.NUMBER;
+ case BOOLEAN: return DataUtil.BOOLEAN;
case LIST: return DataUtil.OBJECT;
case STRING:
default: return DataUtil.STRING;
@@ -722,7 +737,9 @@
/**
* Converts from Flare data types to XGMML types.
*/
- private static function fromCW_Type(type:int):String {
+ private static function fromCW_Type(type:int, value:*=null):String {
+ if (value is Date) return STRING;
+
switch (type) {
case DataUtil.INT: return INTEGER;
case DataUtil.NUMBER: return REAL;
Added:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/error/CWError.as
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/error/CWError.as
(rev 0)
+++ cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/error/CWError.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -0,0 +1,41 @@
+/*
+ This file is part of Cytoscape Web.
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Agilent Technologies
+ - Institut Pasteur
+ - Institute for Systems Biology
+ - Memorial Sloan-Kettering Cancer Center
+ - National Center for Integrative Biomedical Informatics
+ - Unilever
+ - University of California San Diego
+ - University of California San Francisco
+ - University of Toronto
+
+ This library 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 library 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 library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+package org.cytoscapeweb.model.error {
+ public class CWError extends Error {
+
+ public var code:String;
+
+ public function CWError(message:String="", code:String=null) {
+ super(message);
+ this.code = code;
+ this.name = "Cytoscape Web Error";
+ }
+ }
+}
\ No newline at end of file
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/methods/error.as
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/methods/error.as
2011-01-04 20:59:57 UTC (rev 23296)
+++ cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/methods/error.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -29,14 +29,23 @@
*/
package org.cytoscapeweb.model.methods {
import org.cytoscapeweb.ApplicationFacade;
+ import org.cytoscapeweb.model.error.CWError;
import org.puremvc.as3.patterns.observer.Notification;
/**
* Gets a resource bundle string.
*/
- public function error(msg:String, id:*=null, name:String=null,
stackTrace:String=null):void {
+ public function error(err:Error):void {
+ var id:* = (err is CWError) ? CWError(err).code : err.errorID;
+ id = id != null ? ""+id : null;
+
+ var msg:String = err.message;
+ var name:String = err.name;
+ var stackTrace:String = err.getStackTrace();
+
var b:Object = { msg: msg, id: id, name: name, stackTrace: stackTrace
};
var n:Notification = new Notification(ApplicationFacade.ERROR, b);
+
ApplicationFacade.getInstance().notifyObservers(n);
}
}
\ No newline at end of file
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/util/ErrorCodes.as
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/util/ErrorCodes.as
2011-01-04 20:59:57 UTC (rev 23296)
+++ cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/util/ErrorCodes.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -36,6 +36,7 @@
// ========[ CONSTANTS
]====================================================================
+ public static const INVALID_DATA_CONVERSION:String = "dat001";
public static const BROKEN_IMAGE:String = "img001";
// ========[ CONSTRUCTOR
]==================================================================
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/ExternalMediator.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/ExternalMediator.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/ExternalMediator.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -136,7 +136,7 @@
else
return ExternalInterface.call(functionName, argument);
} catch (err:Error) {
- error(err.message, err.errorID, err.name,
err.getStackTrace());
+ error(err);
}
} else {
trace("Error [callExternalInterface]: ExternalInterface is NOT
available!");
@@ -374,7 +374,7 @@
} catch (err:Error) {
trace("[ERROR]: addNode: " + err.getStackTrace());
- error(err.message, err.errorID, err.name, err.getStackTrace());
+ error(err);
}
return o;
@@ -394,7 +394,7 @@
} catch (err:Error) {
trace("[ERROR]: addEdge: " + err.getStackTrace());
- error(err.message, err.errorID, err.name, err.getStackTrace());
+ error(err);
}
return o;
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/render/ImageCache.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/render/ImageCache.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/render/ImageCache.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -44,10 +44,10 @@
import org.cytoscapeweb.model.data.VisualStyleBypassVO;
import org.cytoscapeweb.model.data.VisualStyleVO;
import org.cytoscapeweb.model.data.VizMapperVO;
+ import org.cytoscapeweb.model.error.CWError;
import org.cytoscapeweb.model.methods.error;
import org.cytoscapeweb.util.ErrorCodes;
import org.cytoscapeweb.util.VisualProperties;
- import org.cytoscapeweb.util.methods.$each;
public class ImageCache {
@@ -190,7 +190,7 @@
loader.contentLoaderInfo.addEventListener(IOErrorEvent.IO_ERROR,
function(e:IOErrorEvent):void {trace("ImageCache - Error loading image: " + e);
_broken[url] = true;
- error("Image cannot be loaded: " + url,
ErrorCodes.BROKEN_IMAGE, e.type, e.text);
+ error(new CWError("Image cannot be loaded: "+url+"
("+e.type+"--"+e.text+")", ErrorCodes.BROKEN_IMAGE));
checkOnLoadingEnd();
});
Modified:
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/ExternalObjectConverterTest.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/ExternalObjectConverterTest.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/ExternalObjectConverterTest.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -46,7 +46,7 @@
public function testConvertToDataSet():void {
// Empty networks:
// --------------------------------------------------------------
- var n:*, ds:DataSet, ns:DataSchema, es:DataSchema, nodes:Array,
nd:Array, ed:Array;
+ var network:*, ds:DataSet, ns:DataSchema, es:DataSchema,
nodes:Array, nd:Array, ed:Array;
var networks:Array = [ null,
{},
@@ -54,8 +54,8 @@
{ schema: { nodes: [], edges: [] }, data: {
nodes: [], edges: [] } }
];
- for each (n in networks) {
- ds = ExternalObjectConverter.convertToDataSet(n);
+ for each (network in networks) {
+ ds = ExternalObjectConverter.convertToDataSet(network);
assertMinNodesSchema(ds.nodes.schema);
assertMinEdgesSchema(ds.edges.schema);
assertEmptyGraph(ds);
@@ -63,11 +63,16 @@
// A simple network:
// --------------------------------------------------------------
- n = {
+ var now:Date = new Date();
+
+ network = {
dataSchema: {
nodes: [
{ name: "id", type: "number" }, // WRONG! Should be
string and will be ignored
- { name: "score", type: "number", defValue: -1 }
+ { name: "label", type: "string" },
+ { name: "score", type: "number", defValue: -1 },
+ { name: "ranking", type: "int" },
+ { name: "date", type: "object", defValue: now }
],
edges: [
{ name: "source", type: "string", defValue: "1" },
// Should ignore defValue
@@ -77,46 +82,72 @@
},
data: {
nodes: [
- { id: 1, score: 1.11 }, // Should convert id to string
- { id: "2", score: 2.22 },
- { id: "3", score: 3.33 }
+ { id: "1", label: "Node 1", score: 1.11, date: new
Date(2010, 1, 1) },
+ { id: "2", label: "Node 2", score: 2.22 },
+ { id: "3", label: "Node 3", score: 3.33 }
],
edges: [
{ id: "e1", source: "1", target: "2", weight: 0.5 },
- { id: "e2", source: "2", target: 3, weight: 0.5 }, //
Should convert target to string
- { id: "e3", source: 3, target: "3", weight: 0.25,
directed: false } // Should convert source to string
+ { id: "e2", source: "2", target: "3", weight: 0.5 },
+ { id: "e3", source: "3", target: "3", weight: 0.25,
directed: false }
]
}
};
- ds = ExternalObjectConverter.convertToDataSet(n);
+ ds = ExternalObjectConverter.convertToDataSet(network);
- // Schema:
+ // Test schema:
+ // --------------------
ns = ds.nodes.schema;
es = ds.edges.schema;
+ // Nodes Schema:
assertMinNodesSchema(ns);
+
assertEquals(DataUtil.NUMBER, ns.getFieldByName("score").type);
assertEquals(-1, ns.getFieldByName("score").defaultValue);
+ assertEquals(DataUtil.INT, ns.getFieldByName("ranking").type);
+ assertEquals(0, ns.getFieldByName("ranking").defaultValue);
+
+ assertEquals(DataUtil.STRING, ns.getFieldByName("label").type);
+ assertTrue(null === ns.getFieldByName("label").defaultValue);
+
+ assertEquals(DataUtil.OBJECT, ns.getFieldByName("date").type);
+ assertTrue(now === ns.getFieldByName("date").defaultValue);
+
+ // Edges schema
assertMinEdgesSchema(es, true);
- assertEquals(undefined,
es.getFieldByName(ExternalObjectConverter.SOURCE).defaultValue);
+
+ assertTrue(null ===
es.getFieldByName(ExternalObjectConverter.SOURCE).defaultValue);
+
assertEquals(DataUtil.NUMBER, es.getFieldByName("weight").type);
+ assertTrue(null === es.getFieldByName("weight").defaultValue);
+
assertEquals(DataUtil.BOOLEAN,
es.getFieldByName(ExternalObjectConverter.DIRECTED).type);
- // Data
+ // Test Data:
+ // --------------------
nd = ds.nodes.data;
ed = ds.edges.data;
- assertEquals(n.data.nodes.length, nd.length);
- assertEquals(n.data.edges.length, ed.length);
+ assertEquals(network.data.nodes.length, nd.length);
+ assertEquals(network.data.edges.length, ed.length);
+ for each (var n:Object in nd) {
+ assertTrue(n.id is String);
+ assertTrue(n.label is String);
+ assertTrue(n.score is Number);
+ assertTrue(n.ranking is int);
+ assertTrue(n.date is Date);
+ assertEquals((n.id !== "1"), (n.date == now));
+ }
for each (var e:Object in ed) {
+ assertTrue(e.id is String);
+ assertTrue(e.weight is Number);
+ assertTrue(e.directed is Boolean);
assertEquals(e.id !== "e3", e.directed);
}
-
-
- // TODO: test values!
}
public function testToExtObject():void {
Modified:
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/XGMMLConverterTest.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/XGMMLConverterTest.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/XGMMLConverterTest.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -31,6 +31,7 @@
import flare.data.DataSet;
import flare.data.DataTable;
+ import flare.data.DataUtil;
import flare.vis.data.Data;
import flash.utils.IDataOutput;
@@ -89,7 +90,7 @@
}
}
- public function testParseValue():void {
+ public function testParseGraphicsValue():void {
// Device fonts:
const F1:String = "Default-0-12";
const F2:String = "SansSerif-0-08";
@@ -144,9 +145,25 @@
];
for each (var t:Object in tests) {
- var v:* = XGMMLConverter.parseValue(t.prop, t.value);
+ var v:* = XGMMLConverter.parseGraphicsValue(t.prop, t.value);
assertEquals(t.res, v);
}
}
+
+ public function testParseAttValue():void {
+ var tests:Array = [
+ { value: "0", type: DataUtil.BOOLEAN, res: false },
+ { value: "false", type: DataUtil.BOOLEAN, res: false },
+ { value: "FALSE", type: DataUtil.BOOLEAN, res: false },
+ { value: "1", type: DataUtil.BOOLEAN, res: true },
+ { value: "true", type: DataUtil.BOOLEAN, res: true },
+ { value: "TRUE", type: DataUtil.BOOLEAN, res: true }
+ ];
+
+ for each (var t:Object in tests) {
+ var v:* = XGMMLConverter.parseAttValue(t.value, t.type);
+ assertEquals(t.res, v);
+ }
+ }
}
}
\ No newline at end of file
Modified:
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/view/render/ImageCacheTest.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/view/render/ImageCacheTest.as
2011-01-04 20:59:57 UTC (rev 23296)
+++
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/view/render/ImageCacheTest.as
2011-01-05 00:11:24 UTC (rev 23297)
@@ -101,13 +101,17 @@
}
public function testDispose():void {
- // Initial state:
- assertEquals(1, _cache.size);
- assertFalse(_cache.isLoading());
+ function runTest():void {trace(_cache.size)
+ // Initial state:
+ assertTrue(_cache.size > 0);
+ assertFalse(_cache.isLoading());
+
+ _cache.dispose();
+ assertEquals(0, _cache.size);
+ assertFalse(_cache.isLoading());
+ };
- _cache.dispose();
- assertEquals(0, _cache.size);
- assertFalse(_cache.isLoading());
+ _cache.loadImages(_simpleVs, null, addAsync(runTest, 3000));
}
}
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