Author: scooter
Date: 2008-09-08 10:42:58 -0700 (Mon, 08 Sep 2008)
New Revision: 14848
Modified:
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/driver/Driver.java
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/mapping/MapCPathToCytoscape.java
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/web_service/CPathProtocol.java
Log:
Remove debugging System.out.printlns
Modified:
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/driver/Driver.java
===================================================================
---
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/driver/Driver.java
2008-09-07 04:18:08 UTC (rev 14847)
+++
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/driver/Driver.java
2008-09-08 17:42:58 UTC (rev 14848)
@@ -32,6 +32,7 @@
package org.cytoscape.coreplugin.cpath2.driver;
// imports
+import cytoscape.logger.CyLogger;
import org.cytoscape.coreplugin.cpath2.http.HTTPEvent;
import org.cytoscape.coreplugin.cpath2.http.HTTPServer;
@@ -43,6 +44,7 @@
* @author Benjamin Gross
*/
public class Driver implements HTTPServerListener {
+ CyLogger logger = CyLogger.getLogger(HTTPServerListener.class);
/**
* Our implementation of HTTPServerListener.
@@ -51,7 +53,7 @@
*/
public void httpEvent(HTTPEvent event) {
- System.out.println("request received: " + event.getRequest());
+ logger.debug("request received: " + event.getRequest());
}
public static void main(String[] args) {
@@ -66,4 +68,4 @@
// create server
new HTTPServer(HTTPServer.DEFAULT_PORT, driver, debug).start();
}
-}
\ No newline at end of file
+}
Modified:
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/mapping/MapCPathToCytoscape.java
===================================================================
---
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/mapping/MapCPathToCytoscape.java
2008-09-07 04:18:08 UTC (rev 14847)
+++
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/mapping/MapCPathToCytoscape.java
2008-09-08 17:42:58 UTC (rev 14848)
@@ -97,7 +97,7 @@
}
}
}
- System.out.println("CPATH REQUEST: " + cpathRequest.toString());
+ // System.out.println("CPATH REQUEST: " + cpathRequest.toString());
loadMergeDialog(cpathRequest);
}
@@ -124,4 +124,4 @@
}
cPathProperties.setDownloadMode(downloadMode);
}
-}
\ No newline at end of file
+}
Modified:
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
===================================================================
---
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
2008-09-07 04:18:08 UTC (rev 14847)
+++
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
2008-09-08 17:42:58 UTC (rev 14848)
@@ -6,6 +6,7 @@
import cytoscape.ding.CyGraphLOD;
import cytoscape.layout.CyLayoutAlgorithm;
import cytoscape.layout.CyLayouts;
+import cytoscape.logger.CyLogger;
import cytoscape.view.CyNetworkView;
import cytoscape.data.CyAttributes;
import cytoscape.data.readers.GraphReader;
@@ -53,6 +54,7 @@
private CPathResponseFormat format;
private final static String CPATH_SERVER_NAME_ATTRIBUTE =
"CPATH_SERVER_NAME";
private final static String CPATH_SERVER_DETAILS_URL =
"CPATH_SERVER_DETAILS_URL";
+ private CyLogger logger =
CyLogger.getLogger(ExecuteGetRecordByCPathId.class);
/**
* Constructor.
@@ -410,14 +412,14 @@
}
ArrayList batchList = createBatchArray(cyNetwork);
if (batchList.size()==0) {
- System.out.println ("Skipping node details. Already have all the
details new need.");
+ logger.info ("Skipping node
details. Already have all the details new need.");
}
for (int i=0; i<batchList.size(); i++) {
if (haltFlag == true) {
break;
}
ArrayList currentList = (ArrayList) batchList.get(i);
- System.out.println ("Getting node details, batch: " + i);
+ logger.debug ("Getting node details, batch: " + i);
long ids[] = new long [currentList.size()];
for (int j=0; j<currentList.size(); j++) {
CyNode node = (CyNode) currentList.get(j);
@@ -535,4 +537,4 @@
public void setStatus(String string) throws IllegalThreadStateException,
NullPointerException {
}
-}
\ No newline at end of file
+}
Modified:
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/web_service/CPathProtocol.java
===================================================================
---
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/web_service/CPathProtocol.java
2008-09-07 04:18:08 UTC (rev 14847)
+++
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/web_service/CPathProtocol.java
2008-09-08 17:42:58 UTC (rev 14848)
@@ -10,6 +10,7 @@
import org.jdom.Document;
import org.jdom.JDOMException;
import org.jdom.Element;
+import cytoscape.logger.CyLogger;
import cytoscape.task.TaskMonitor;
import cytoscape.util.ProxyHandler;
@@ -156,6 +157,7 @@
private volatile HttpMethodBase method;
private boolean cancelledByUser = false;
private static boolean debug = false;
+ private CyLogger logger =
CyLogger.getLogger(CPathProtocol.class);
/**
* Constructor.
@@ -251,12 +253,12 @@
nvps = createNameValuePairs(true);
method = new PostMethod(baseUrl);
((PostMethod)(method)).addParameters(nvps);
- System.out.println("Connect: " + method.getURI() + " (via
POST)");
+ logger.info("Connect: " + method.getURI() + " (via POST)");
} else {
nvps = createNameValuePairs(false);
String liveUrl = createURI(baseUrl, nvps);
method = new GetMethod(liveUrl);
- System.out.println("Connect: " + liveUrl);
+ logger.info("Connect: " + liveUrl);
}
int statusCode = client.executeMethod(method);
@@ -330,7 +332,7 @@
// proxy.server.type=HTTP
if (proxyServer != null) {
String proxyAddress = proxyServer.toString();
- System.out.println("full proxy string: " + proxyAddress);
+ if (debug) logger.debug("full proxy string: " + proxyAddress);
String[] addressComponents = proxyAddress.split("@");
if (addressComponents.length == 2) {
String parts[] = addressComponents[1].split(":");
@@ -340,8 +342,8 @@
if (hostParts.length > 0) {
String host = hostParts[0].trim();
String port = parts[1].trim();
- System.out.println ("proxy host: " + host);
- System.out.println("proxy port: " + port);
+ if (debug) logger.debug("proxy host: " + host);
+ if (debug) logger.debug("proxy port: " + port);
client.getHostConfiguration().setProxy(host,
Integer.parseInt(port));
}
}
@@ -442,4 +444,4 @@
}
}
}
-}
\ No newline at end of file
+}
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