Author: clopes
Date: 2012-08-13 15:04:21 -0700 (Mon, 13 Aug 2012)
New Revision: 30178
Added:
core3/impl/trunk/io-impl/impl/src/test/resources/testData/xgmml/bare_ampersands.xgmml
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReader.java
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
Log:
Fixes #1289 : system property "cytoscape.xgmml.repair.bare.ampersands" is now
supported by Cytoscape 3
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReader.java
2012-08-13 21:15:44 UTC (rev 30177)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReader.java
2012-08-13 22:04:21 UTC (rev 30178)
@@ -29,6 +29,7 @@
import java.io.IOException;
import java.io.InputStream;
+import java.io.PushbackInputStream;
import java.util.Collection;
import java.util.List;
import java.util.Map;
@@ -66,6 +67,8 @@
public class GenericXGMMLReader extends AbstractNetworkReader {
+ public static final String REPAIR_BARE_AMPERSANDS_PROPERTY =
"cytoscape.xgmml.repair.bare.ampersands";
+
protected final ReadDataManager readDataMgr;
protected final XGMMLParser parser;
protected final UnrecognizedVisualPropertyManager
unrecognizedVisualPropertyMgr;
@@ -74,17 +77,24 @@
private static final Logger logger =
LoggerFactory.getLogger(GenericXGMMLReader.class);
public GenericXGMMLReader(final InputStream inputStream,
- final
CyNetworkViewFactory cyNetworkViewFactory,
- final
CyNetworkFactory cyNetworkFactory,
- final
RenderingEngineManager renderingEngineMgr,
- final
ReadDataManager readDataMgr,
- final XGMMLParser
parser,
- final
UnrecognizedVisualPropertyManager unrecognizedVisualPropertyMgr) {
+ final
CyNetworkViewFactory cyNetworkViewFactory,
+ final
CyNetworkFactory cyNetworkFactory,
+ final
RenderingEngineManager renderingEngineMgr,
+ final ReadDataManager
readDataMgr,
+ final XGMMLParser
parser,
+ final
UnrecognizedVisualPropertyManager unrecognizedVisualPropertyMgr) {
super(inputStream, cyNetworkViewFactory, cyNetworkFactory);
this.readDataMgr = readDataMgr;
this.parser = parser;
this.unrecognizedVisualPropertyMgr =
unrecognizedVisualPropertyMgr;
this.visualLexicon =
renderingEngineMgr.getDefaultVisualLexicon();
+
+ // This should only be used when an XGMML file or session
cannot be read due to improperly encoded ampersands,
+ // as it slows down the reading process.
+ final boolean attemptRepair =
Boolean.getBoolean(REPAIR_BARE_AMPERSANDS_PROPERTY);
+
+ if (attemptRepair)
+ this.inputStream = new
RepairBareAmpersandsInputStream(inputStream, 512);
}
@Override
@@ -289,4 +299,83 @@
return s;
}
+
+ private static class RepairBareAmpersandsInputStream extends
PushbackInputStream {
+ private final byte[] encodedAmpersand = new byte[] { 'a', 'm',
'p', ';' };
+
+ public RepairBareAmpersandsInputStream(final InputStream in) {
+ super(in);
+ }
+
+ public RepairBareAmpersandsInputStream(final InputStream in,
final int size) {
+ super(in, size);
+ }
+
+ @Override
+ public int read() throws IOException {
+ int c;
+
+ c = super.read();
+ if (c == (int) '&') {
+ byte[] b = new byte[7];
+ int cnt;
+
+ cnt = read(b);
+ if (cnt > 0) {
+ boolean isEntity;
+ int i;
+
+ isEntity = false;
+ i = 0;
+ while ((i < cnt) && (!isEntity)) {
+ isEntity = (b[i] == ';');
+ i++;
+ }
+
+ byte[] pb = new byte[cnt];
+ for (int p = 0; p < cnt; p++) {
+ pb[p] = b[p];
+ }
+ unread(pb);
+
+ if (!isEntity) {
+ unread(encodedAmpersand);
+ }
+ }
+ }
+
+ return c;
+ }
+
+ @Override
+ public int read(byte[] b, int off, int len) throws IOException {
+ if (b == null) {
+ throw new NullPointerException();
+ } else if (off < 0 || len < 0 || len > b.length - off) {
+ throw new IndexOutOfBoundsException();
+ } else if (len == 0) {
+ return 0;
+ }
+
+ int cnt;
+ int c = -1;
+
+ cnt = 0;
+ while (cnt < len) {
+ c = read();
+ if (c == -1) {
+ break;
+ }
+ b[off] = (byte) c;
+ off++;
+ cnt++;
+ }
+
+ if ((c == -1) && (cnt == 0)) {
+ cnt = -1;
+ }
+
+ return cnt;
+ }
+ }
}
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
2012-08-13 21:15:44 UTC (rev 30177)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
2012-08-13 22:04:21 UTC (rev 30178)
@@ -11,6 +11,7 @@
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
@@ -321,6 +322,22 @@
assertEquals("SansSerif,bold,12",
GenericXGMMLReader.convertOldFontValue("SansSerif,bold,12"));
}
+ @Test(expected=IOException.class)
+ public void testRepairBareAmpersandsPropertyFalse() throws Exception {
+
System.setProperty(GenericXGMMLReader.REPAIR_BARE_AMPERSANDS_PROPERTY, "false");
+ getViews("bare_ampersands.xgmml");
+ }
+
+ @Test
+ public void testRepairBareAmpersandsPropertyTrue() throws Exception {
+
System.setProperty(GenericXGMMLReader.REPAIR_BARE_AMPERSANDS_PROPERTY, "true");
+ List<CyNetworkView> views = getViews("bare_ampersands.xgmml");
+ CyNetwork net = checkSingleNetwork(views, 1, 1);
+ assertEquals("&ABC", net.getRow(net).get("&net_att_1",
String.class));
+ assertEquals("CDE&",
net.getRow(net.getNodeList().get(0)).get("node_att_$1", String.class));
+ assertEquals(25,
net.getRow(net.getEdgeList().get(0)).get("edge_att_1$",
Integer.class).intValue());
+ }
+
private void assertCustomColumnsAreMutable(CyNetwork net) {
// User or non-default columns should be immutable
List<CyTable> tables = new ArrayList<CyTable>();
Added:
core3/impl/trunk/io-impl/impl/src/test/resources/testData/xgmml/bare_ampersands.xgmml
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/resources/testData/xgmml/bare_ampersands.xgmml
(rev 0)
+++
core3/impl/trunk/io-impl/impl/src/test/resources/testData/xgmml/bare_ampersands.xgmml
2012-08-13 22:04:21 UTC (rev 30178)
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<graph label="Network A" xmlns:dc="http://purl.org/dc/elements/1.1/";
+ xmlns:xlink="http://www.w3.org/1999/xlink";
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#";
+ xmlns:cy="http://www.cytoscape.org"; xmlns="http://www.cs.rpi.edu/XGMML";
+ directed="1">
+
+ <att type="string" name="&net_att_1" value="&ABC"/>
+
+ <node label="node1" id="1">
+ <att type="string" name="node_att_$1" value="CDE&" />
+ </node>
+ <edge label="node1 (DirectedEdge) node1" source="1" target="1">
+ <att type="integer" name="edge_att_1$" value="25" />
+ </edge>
+</graph>
\ No newline at end of file
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