Author: mes
Date: 2012-07-19 16:00:04 -0700 (Thu, 19 Jul 2012)
New Revision: 29930
Modified:
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromURL.java
Log:
support for format conversion through URLs
Modified:
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2012-07-19 22:59:01 UTC (rev 29929)
+++
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2012-07-19 23:00:04 UTC (rev 29930)
@@ -125,13 +125,22 @@
}
public static File downloadToTempFile(String urlString) {
+ return downloadToTempFile(urlString,null);
+ }
+
+ public static File downloadToTempFile(String urlString, GSDataFormat
format) {
InputStream is = null;
OutputStream os = null;
File tempFile = null;
try {
URL url = new URL(urlString);
DataManagerClient dmc =
getSession().getDataManagerClient();
- is = dmc.getInputStream(url);
+
+ if ( format == null )
+ is = dmc.getInputStream(url);
+ else
+ is =
dmc.getInputStream(dmc.getFileUrl(url,format.getUrl()));
+
tempFile = File.createTempFile("tempGS","." +
getExtension(url.toString()));
os =new FileOutputStream(tempFile);
byte buf[] = new byte[1024];
Modified:
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromURL.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromURL.java
2012-07-19 22:59:01 UTC (rev 29929)
+++
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromURL.java
2012-07-19 23:00:04 UTC (rev 29930)
@@ -9,6 +9,7 @@
import org.genomespace.sws.GSLoadEventListener;
import org.genomespace.sws.GSLoadEvent;
+import org.genomespace.datamanager.core.GSDataFormat;
public class LoadNetworkFromURL implements GSLoadEventListener {
private static final CyLogger logger =
CyLogger.getLogger(LoadNetworkFromURL.class);
@@ -24,7 +25,13 @@
return;
try {
- File tmp = GSUtils.downloadToTempFile(netURL);
+
+ final String ext = GSUtils.getExtension(netURL);
+ GSDataFormat dataFormat = null;
+ if ( ext != null && ext.equalsIgnoreCase("adj") )
+ dataFormat =
GSUtils.findConversionFormat(GSUtils.getSession().getDataManagerClient().listDataFormats(),
"xgmml");
+
+ File tmp =
GSUtils.downloadToTempFile(netURL,dataFormat);
Cytoscape.createNetworkFromFile(tmp.getPath()).setTitle(netURL);
} catch ( Exception e ) { e.printStackTrace(); }
}
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