Author: mes
Date: 2011-02-25 19:03:22 -0800 (Fri, 25 Feb 2011)
New Revision: 24244
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/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/ListFilesInGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java
Log:
it compiles
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
2011-02-26 02:24:27 UTC (rev 24243)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
2011-02-26 03:03:22 UTC (rev 24244)
@@ -13,8 +13,9 @@
import java.util.Map;
import java.util.Collection;
-import org.genomespace.client.GsFile;
+import org.genomespace.datamanager.core.GSFileMetadata;
import org.genomespace.client.GsSession;
+import org.genomespace.client.DataManagerClient;
import org.genomespace.client.User;
/**
@@ -42,22 +43,22 @@
try {
// login to GenomeSpace
- GsSession session = new GsSession();
+ GsSession client = new GsSession();
String username = "test";
String password = "password";
- User user = session.login(username, password);
- logger.info("Logged in to GenomeSpace: " + session.isLoggedIn()
+ " as " + user.getUsername());
+ User user = client.login(username, password);
+ logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+ DataManagerClient dmc = client.getDataManagerClient();
// list the files present for this user
- DataManagerClient dmClient = gsSession.getDataManagerClient();
- GSDirectoryListing homeDirInfo =
dmClient.listDefaultDirectory();
+ Map<String,GSFileMetadata> files = GSUtils.getFileNameMap(
dmc.listDefaultDirectory().getContents() );
- String selectedFile = getSelectedFile( homeDirInfo.get list of
files );
+ String selectedFile = getSelectedFile( files.keySet() );
// Delete the file from GenomeSpace
if (selectedFile != null && files.get(selectedFile) != null) {
logger.info("Deleting " + selectedFile);
- client.delete(files.get(selectedFile));
+ dmc.delete(files.get(selectedFile));
}
} catch (Exception ex) {
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
2011-02-26 02:24:27 UTC (rev 24243)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
2011-02-26 03:03:22 UTC (rev 24244)
@@ -13,8 +13,9 @@
import java.util.Map;
import java.util.Collection;
-import org.genomespace.client.GsFile;
+import org.genomespace.datamanager.core.GSFileMetadata;
import org.genomespace.client.GsSession;
+import org.genomespace.client.DataManagerClient;
import org.genomespace.client.User;
/**
@@ -47,17 +48,19 @@
String password = "password";
User user = client.login(username, password);
logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+ DataManagerClient dmc = client.getDataManagerClient();
// list the files present for this user
- Map<String,GsFile> files = GSUtils.getFileNameMap(
client.list() );
+ Map<String,GSFileMetadata> files = GSUtils.getFileNameMap(
dmc.listDefaultDirectory().getContents() );
String selectedFile = getSelectedFile( files.keySet() );
// Download the file back from GenomeSpace
if (selectedFile != null && files.get(selectedFile) != null) {
logger.info("Downloading " + files.get(selectedFile));
- GsFile localCopy =
client.downloadFile(files.get(selectedFile));
- logger.info("\t saved to: " +
localCopy.getFile().getAbsolutePath());
+ File localCopy = new File(selectedFile);
+ dmc.downloadFile(files.get(selectedFile), localCopy,
true);
+ logger.info("\t saved to: " +
localCopy.getAbsolutePath());
}
} catch (Exception ex) {
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
2011-02-26 02:24:27 UTC (rev 24243)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2011-02-26 03:03:22 UTC (rev 24244)
@@ -5,18 +5,20 @@
import java.util.List;
import java.util.Map;
import java.util.HashMap;
+import java.util.Collection;
-import org.genomespace.client.GsFile;
+import org.genomespace.datamanager.core.GSFileMetadata;
final class GSUtils {
private GSUtils() {};
- public static Map<String,GsFile> getFileNameMap(List<GsFile> l) {
- Map<String,GsFile> nm = new HashMap<String,GsFile>();
- for ( GsFile f : l )
- nm.put(f.getFilename(), f);
+ public static Map<String,GSFileMetadata>
getFileNameMap(Collection<GSFileMetadata> l) {
+ Map<String,GSFileMetadata> nm = new
HashMap<String,GSFileMetadata>();
+ for ( GSFileMetadata f : l )
+ nm.put(f.getName(), f);
return nm;
}
}
+
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
2011-02-26 02:24:27 UTC (rev 24243)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
2011-02-26 03:03:22 UTC (rev 24244)
@@ -17,8 +17,9 @@
import java.util.List;
import java.util.Vector;
-import org.genomespace.client.GsFile;
+import org.genomespace.datamanager.core.GSFileMetadata;
import org.genomespace.client.GsSession;
+import org.genomespace.client.DataManagerClient;
import org.genomespace.client.User;
/**
@@ -51,13 +52,14 @@
String password = "password";
User user = client.login(username, password);
logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+ DataManagerClient dmc = client.getDataManagerClient();
// list the files present for this user
- List<GsFile> myFiles = client.list();
+ List<GSFileMetadata> myFiles =
dmc.listDefaultDirectory().getContents();
logger.info("Files on GenomeSpace for " + user.getUsername());
Vector<String> fileNames = new Vector<String>();
- for (GsFile aFile: myFiles) {
- fileNames.add(aFile.getFilename());
+ for (GSFileMetadata aFile: myFiles) {
+ fileNames.add(aFile.getName());
}
displayFiles(fileNames);
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
2011-02-26 02:24:27 UTC (rev 24243)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java
2011-02-26 03:03:22 UTC (rev 24244)
@@ -11,7 +11,9 @@
import java.awt.FileDialog;
import java.util.List;
-import org.genomespace.client.GsFile;
+import org.genomespace.datamanager.core.GSFileMetadata;
+import org.genomespace.datamanager.core.GSFileMetadataImpl;
+import org.genomespace.client.DataManagerClient;
import org.genomespace.client.GsSession;
import org.genomespace.client.User;
@@ -47,9 +49,10 @@
String password = "password";
User user = client.login(username, password);
logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+ DataManagerClient dmc = client.getDataManagerClient();
- GsFile gsf = new GsFile(f);
- client.uploadFile(gsf);
+ // TODO add metadata info?
+ dmc.uploadFile(f, new GSFileMetadataImpl());
} catch (Exception ex) {
logger.error("GenomeSpace failed",ex);
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