Author: jm
Date: 2011-07-19 14:06:23 -0700 (Tue, 19 Jul 2011)
New Revision: 26216
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
Log:
Fixes #269: Implemented virtual column serialization/deserialization
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
2011-07-19 21:05:12 UTC (rev 26215)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
2011-07-19 21:06:23 UTC (rev 26216)
@@ -38,11 +38,12 @@
import java.io.FileInputStream;
import java.io.IOException;
import java.io.OutputStream;
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@@ -51,16 +52,20 @@
import java.util.zip.ZipOutputStream;
import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.internal.util.session.SessionUtil;
+import org.cytoscape.io.internal.util.session.VirtualColumnSerializer;
import org.cytoscape.io.internal.write.xgmml.XGMMLWriter;
import org.cytoscape.io.write.CyNetworkViewWriterManager;
import org.cytoscape.io.write.CyPropertyWriterManager;
import org.cytoscape.io.write.CyTableWriterManager;
import org.cytoscape.io.write.CyWriter;
import org.cytoscape.io.write.VizmapWriterManager;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTable.SavePolicy;
import org.cytoscape.model.CyTableMetadata;
-import org.cytoscape.model.CyTable.SavePolicy;
+import org.cytoscape.model.VirtualColumnInfo;
import org.cytoscape.property.session.Cysession;
import org.cytoscape.session.CySession;
import org.cytoscape.view.model.CyNetworkView;
@@ -86,9 +91,6 @@
*/
public class SessionWriterImpl extends AbstractTask implements CyWriter {
- // These values will be replaced.
- private static final char[] INVALID_CHAR = { '[', '\\', '/', ':', '*',
'?', '"', '<', '>', '|', ']'};
-
// Enumerate types (node & edge)
public static final int NODE = 1;
public static final int EDGE = 2;
@@ -122,6 +124,7 @@
private final CyFileFilter propertiesFilter;
private final CyFileFilter tableFilter;
private final CyFileFilter vizmapFilter;
+ private Map<Long, String> tableFilenamesBySUID;
public SessionWriterImpl(final OutputStream outputStream,
final CySession session,
@@ -169,7 +172,8 @@
for (CyNetworkView netView : session.getNetworkViews())
zipNetwork(netView);
- zipGlobalTables();
+ zipTables();
+ zipVirtualColumns();
zipCySession();
zipVizmap();
zipCytoscapeProps();
@@ -179,6 +183,39 @@
zos.close();
}
+ private void zipVirtualColumns() throws IOException {
+ zos.putNextEntry(new ZipEntry(sessionDir +
SessionUtil.CYTABLE_METADATA_FILE));
+ PrintWriter writer = new PrintWriter(new
OutputStreamWriter(zos, "UTF-8"));
+ try {
+ for (CyTableMetadata metadata : session.getTables()) {
+ CyTable table = metadata.getCyTable();
+ String targetTable =
tableFilenamesBySUID.get(table.getSUID());
+ if (targetTable == null) {
+ continue;
+ }
+ for (CyColumn column : table.getColumns()) {
+ VirtualColumnInfo info =
column.getVirtualColumnInfo();
+ if (!info.isVirtual()) {
+ continue;
+ }
+ String sourceTable =
tableFilenamesBySUID.get(info.getSourceTable().getSUID());
+ VirtualColumnSerializer serializer =
new VirtualColumnSerializer(
+ column.getName(),
+ sourceTable,
+ targetTable,
+ info.getSourceColumn(),
+ info.getSourceJoinKey(),
+ info.getTargetJoinKey(),
+ info.isImmutable());
+ serializer.serialize(writer);
+ }
+ }
+ } finally {
+ writer.flush();
+ zos.closeEntry();
+ }
+ }
+
/**
* Writes the vizmap.props file to the session zip.
*/
@@ -227,7 +264,7 @@
private void zipNetwork(final CyNetworkView view) throws Exception {
final CyNetwork network = view.getModel();
- String xgmmlFile = getNetworkFileName(network) + XGMML_EXT;
+ String xgmmlFile = SessionUtil.getNetworkFileName(network) +
XGMML_EXT;
zos.putNextEntry(new ZipEntry(sessionDir + xgmmlFile) );
CyWriter writer = networkViewWriterMgr.getWriter(view,
xgmmlFilter, zos);
@@ -243,10 +280,6 @@
writer = null;
}
- private String getNetworkFileName(CyNetwork network) throws
UnsupportedEncodingException {
- return escape(network.getCyRow().get("name", String.class));
- }
-
/**
* Create cysession.xml file.
*
@@ -307,23 +340,8 @@
}
}
- /**
- * Utility to replace invalid chars in the XGMML file name.<br>
- *
- * @param fileName Original file name directly taken from the title.
- * @return Modified file name without invalid chars.
- */
- private String getValidFileName(String fileName) {
- String newFileName = fileName;
- Integer i = 0;
-
- for(Character ch : INVALID_CHAR)
- newFileName = newFileName.replace(ch.toString(),
(i++).toString());
-
- return newFileName;
- }
-
- private void zipGlobalTables() throws Exception {
+ private void zipTables() throws Exception {
+ tableFilenamesBySUID = new HashMap<Long, String>();
Set<CyNetworkView> views = session.getNetworkViews();
Set<CyNetwork> includedNetworks = new HashSet<CyNetwork>();
@@ -341,7 +359,7 @@
continue;
}
- String tableTitle = escape(table.getTitle());
+ String tableTitle =
SessionUtil.escape(table.getTitle());
String fileName;
Set<CyNetwork> networks = metadata.getCyNetworks();
@@ -354,12 +372,10 @@
continue;
}
- String networkFileName =
getNetworkFileName(network);
- String namespace =
escape(metadata.getNamespace());
- String type =
escape(metadata.getType().getCanonicalName());
- fileName = String.format("%s/%s-%s-%s.cytable",
networkFileName, namespace, type, tableTitle);
+ fileName =
SessionUtil.getNetworkTableFilename(network, metadata);
}
+ tableFilenamesBySUID.put(table.getSUID(), fileName);
zos.putNextEntry(new ZipEntry(sessionDir + fileName));
try {
@@ -379,9 +395,4 @@
}
return null;
}
-
- private String escape(String text) throws UnsupportedEncodingException {
- return URLEncoder.encode(text, "UTF-8").replace("-", "%2D");
- }
-
}
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