Author: mes
Date: 2011-02-28 16:05:40 -0800 (Mon, 28 Feb 2011)
New Revision: 24270
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java
Log:
updates and now working in 2.8.2
Modified: csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml 2011-02-28 23:59:35 UTC
(rev 24269)
+++ csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml 2011-03-01 00:05:40 UTC
(rev 24270)
@@ -75,13 +75,11 @@
<artifactId>dm-messages</artifactId>
<version>1.0-beta2</version>
</dependency>
- <!--
<dependency>
<groupId>cytoscape-temp</groupId>
- <artifactId>gs-common-util</artifactId>
- <version>1.0-beta1</version>
+ <artifactId>atm-messages</artifactId>
+ <version>1.0-beta2</version>
</dependency>
- -->
</dependencies>
<repositories>
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
2011-02-28 23:59:35 UTC (rev 24269)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
2011-03-01 00:05:40 UTC (rev 24270)
@@ -42,12 +42,7 @@
try {
- // login to GenomeSpace
- GsSession client = new GsSession();
- String username = "test";
- String password = "password";
- User user = client.login(username, password);
- logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+ GsSession client = GSUtils.getSession();
DataManagerClient dmc = client.getDataManagerClient();
// list the files present for this user
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
2011-02-28 23:59:35 UTC (rev 24269)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
2011-03-01 00:05:40 UTC (rev 24270)
@@ -42,12 +42,7 @@
try {
- // login to GenomeSpace
- GsSession client = new GsSession();
- String username = "test";
- String password = "password";
- User user = client.login(username, password);
- logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+ GsSession client = GSUtils.getSession();
DataManagerClient dmc = client.getDataManagerClient();
// list the files present for this user
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2011-02-28 23:59:35 UTC (rev 24269)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2011-03-01 00:05:40 UTC (rev 24270)
@@ -7,12 +7,30 @@
import java.util.HashMap;
import java.util.Collection;
+import org.genomespace.client.GsSession;
+import org.genomespace.client.exceptions.GSClientException;
+import org.genomespace.client.User;
+
import org.genomespace.datamanager.core.GSFileMetadata;
final class GSUtils {
private GSUtils() {};
+ private static GsSession session = null;
+
+ public static GsSession getSession() {
+ if ( session == null || !session.isLoggedIn()) {
+ try {
+ session = new GsSession();
+ String username = "test";
+ String password = "password";
+ User user = session.login(username, password);
+ } catch (Exception e) { throw new
GSClientException("failed to login",e); }
+ }
+ return session;
+ }
+
public static Map<String,GSFileMetadata>
getFileNameMap(Collection<GSFileMetadata> l) {
Map<String,GSFileMetadata> nm = new
HashMap<String,GSFileMetadata>();
for ( GSFileMetadata f : l )
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java
2011-02-28 23:59:35 UTC (rev 24269)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java
2011-03-01 00:05:40 UTC (rev 24270)
@@ -28,6 +28,5 @@
ListFilesInGenomeSpace listAction = new
ListFilesInGenomeSpace();
Cytoscape.getDesktop().getCyMenus().addAction(listAction);
-
}
}
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
2011-02-28 23:59:35 UTC (rev 24269)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
2011-03-01 00:05:40 UTC (rev 24270)
@@ -46,17 +46,11 @@
try {
- // login to GenomeSpace
- GsSession client = new GsSession();
- String username = "test";
- String password = "password";
- User user = client.login(username, password);
- logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+ GsSession client = GSUtils.getSession();
DataManagerClient dmc = client.getDataManagerClient();
// list the files present for this user
List<GSFileMetadata> myFiles =
dmc.listDefaultDirectory().getContents();
- logger.info("Files on GenomeSpace for " + user.getUsername());
Vector<String> fileNames = new Vector<String>();
for (GSFileMetadata aFile: myFiles) {
fileNames.add(aFile.getName());
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java
2011-02-28 23:59:35 UTC (rev 24269)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java
2011-03-01 00:05:40 UTC (rev 24270)
@@ -44,11 +44,7 @@
if ( f == null )
return;
- GsSession client = new GsSession();
- String username = "test";
- String password = "password";
- User user = client.login(username, password);
- logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+ GsSession client = GSUtils.getSession();
DataManagerClient dmc = client.getDataManagerClient();
// TODO add metadata info?
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
