Author: scooter
Date: 2010-11-02 11:38:23 -0700 (Tue, 02 Nov 2010)
New Revision: 22682
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/BioCycPlugin.java
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/commands/QueryHandler.java
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/model/Database.java
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClient.java
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClientGui.java
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycRESTClient.java
Log:
Fix URL reader and support database defaults.
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/BioCycPlugin.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/BioCycPlugin.java
2010-11-02 02:06:30 UTC (rev 22681)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/BioCycPlugin.java
2010-11-02 18:38:23 UTC (rev 22682)
@@ -39,14 +39,21 @@
import cytoscape.plugin.CytoscapePlugin;
import cytoscape.logger.CyLogger;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
import java.util.Properties;
import bioCycPlugin.commands.BioCycCommandHandler;
import bioCycPlugin.webservices.BioCycClient;
-public class BioCycPlugin extends CytoscapePlugin {
+public class BioCycPlugin extends CytoscapePlugin implements
PropertyChangeListener {
private CyLogger logger = null;
private BioCycClient wpclient;
+ private static Properties defaultProps = null;
protected static final String WEBSERVICE_URL = "biocyc.webservice.uri";
// protected static final String DEFAULT_URL =
"http://brg-preview.ai.sri.com/";;
@@ -65,18 +72,59 @@
logger.error(e.getMessage());
}
+ // Listen for exits
+
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.CYTOSCAPE_EXIT,
this);
+
// Setup any global properties
Properties p = CytoscapeInit.getProperties();
if (p.get(WEBSERVICE_URL) == null) {
p.put(WEBSERVICE_URL, DEFAULT_URL);
}
+
+ // Initialize our properties file
+ initBioCycProps();
+
// Register ourselves with the web services infrastructure
wpclient = new BioCycClient(logger);
WebServiceClientManager.registerClient(wpclient);
+ }
+ public static void initBioCycProps() {
+ if (defaultProps == null) {
+ defaultProps = new Properties();
+ File propsFile = new
File(CytoscapeInit.getConfigVersionDirectory(), "bioCycPlugin.props");
+ if (propsFile != null) {
+ try {
+ FileInputStream inputStream = new
FileInputStream(propsFile);
+ defaultProps.load(inputStream);
+ } catch (IOException e) {}
+ }
+ }
}
+ public static String getProp(String prop) {
+ if (defaultProps != null)
+ return defaultProps.getProperty(prop);
+ return null;
+ }
+
+ public static void setProp(String propName, String propValue) {
+ defaultProps.setProperty(propName, propValue);
+ }
+
public static String getBaseUrl() {
return
CytoscapeInit.getProperties().getProperty(WEBSERVICE_URL);
}
+
+ public void propertyChange(PropertyChangeEvent evt) {
+ if (evt.getPropertyName().equals(Cytoscape.CYTOSCAPE_EXIT)) {
+ File propsFile = new
File(CytoscapeInit.getConfigVersionDirectory(), "bioCycPlugin.props");
+ if (propsFile != null) {
+ try {
+ defaultProps.store(new
FileOutputStream(propsFile), "");
+ } catch (IOException e) {}
+ }
+ }
+ }
+
}
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/commands/QueryHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/commands/QueryHandler.java
2010-11-02 02:06:30 UTC (rev 22681)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/commands/QueryHandler.java
2010-11-02 18:38:23 UTC (rev 22682)
@@ -125,6 +125,12 @@
ImportHandler inputHandler = Cytoscape.getImportHandler();
try {
+ // Add a listener so we can fix up some attributes
+ Cytoscape.getPropertyChangeSupport()
+ .addPropertyChangeListener(
Cytoscape.NETWORK_LOADED, new ParseCMLAttributes(logger) );
+ LoadNetworkTask.loadURL(new URL(baseUrl+queryString),
false);
+
+/*
File rawFile = inputHandler.downloadFromURL(new
URL(baseUrl+queryString), null);
File bioPaxFile = new
File(rawFile.getAbsolutePath()+".xml");
rawFile.renameTo(bioPaxFile);
@@ -133,8 +139,11 @@
.addPropertyChangeListener(
Cytoscape.NETWORK_LOADED, new ParseCMLAttributes(logger) );
LoadNetworkTask.loadFile(bioPaxFile, false);
+ logger.info("Loading file into:
"+bioPaxFile.getAbsolutePath());
bioPaxFile.delete();
+*/
} catch (Exception e) {
+ logger.error("Error loading network from
"+baseUrl+queryString+": "+e.getMessage(), e);
throw new MalformedURLException("Unable to load network
from "+baseUrl+queryString+" ("+e.getMessage()+")");
}
}
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/model/Database.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/model/Database.java
2010-11-02 02:06:30 UTC (rev 22681)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/model/Database.java
2010-11-02 18:38:23 UTC (rev 22682)
@@ -32,6 +32,8 @@
*/
package bioCycPlugin.model;
+import bioCycPlugin.BioCycPlugin;
+
import java.util.ArrayList;
import java.util.List;
import org.w3c.dom.Document;
@@ -84,4 +86,17 @@
}
return databases;
}
+
+ public static Database getDefaultDatabase(List<Database>databases) {
+ String db = BioCycPlugin.getProp("defaultDatabase");
+ for (Database d: databases) {
+ if (d.getOrgID().equals(db))
+ return d;
+ }
+ return null;
+ }
+
+ public static void setDefaultDatabase(Database database) {
+ BioCycPlugin.setProp("defaultDatabase", database.getOrgID());
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClient.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClient.java
2010-11-02 02:06:30 UTC (rev 22681)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClient.java
2010-11-02 18:38:23 UTC (rev 22682)
@@ -115,41 +115,6 @@
}
}
- public List<JMenuItem> getNodeContextMenuItems(NodeView nv) {
- List<JMenuItem> menuList = new ArrayList<JMenuItem>();
-
- //Add an item to find interactions
- // menuList.add(new JMenuItem(new NodeInteractionsAction(this,
nv)));
-
- //If the node is a found interaction, add items to open the
source on WP
- CyAttributes attr = Cytoscape.getNodeAttributes();
- String nid = nv.getNode().getIdentifier();
- // addPathwayMenuItems(attr, nid, menuList);
- return menuList;
- }
-
- public List<JMenuItem> getEdgeContextMenuItems(EdgeView ev) {
- List<JMenuItem> menuList = new ArrayList<JMenuItem>();
-
- //If the edge is a found interaction, add items to open the
source on WP
- CyAttributes attr = Cytoscape.getEdgeAttributes();
- String eid = ev.getEdge().getIdentifier();
- // addPathwayMenuItems(attr, eid, menuList);
-
- return menuList;
- }
-
- /**
- * Adds menu items to open and import pathways based on the pathway info
- * stored in the attributes (by the find interactions function).
- * @param attr The attribute store
- * @param nid The node or edge id
- * @param menuList The list to add the menu items to
- */
- private void addPathwayMenuItems(CyAttributes attr, String nid,
List<JMenuItem> menuList) {
- // TODO
- }
-
public void executeService(CyWebServiceEvent e)
throws CyWebServiceException {
if(CLIENT_ID.equals(e.getSource())) {
@@ -237,10 +202,6 @@
}
public void halt() {
- //Not 2.6 compatible
- //
WebServiceClientManager.getCyWebServiceEventSupport().fireCyWebServiceEvent(
- // new
CyWebServiceEvent(CLIENT_ID, WSEventType.CANCEL, query)
- // );
}
public void setTaskMonitor(TaskMonitor m)
@@ -250,10 +211,6 @@
public void executeService(CyWebServiceEvent event)
throws CyWebServiceException {
- //Not 2.6 compatible
- // if
(event.getEventType().equals(WSEventType.CANCEL)) {
- // throw new
CyWebServiceException(CyWebServiceException.WSErrorCode.REMOTE_EXEC_FAILED);
- // }
}
}
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClientGui.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClientGui.java
2010-11-02 02:06:30 UTC (rev 22681)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClientGui.java
2010-11-02 18:38:23 UTC (rev 22682)
@@ -16,9 +16,9 @@
//
package bioCycPlugin.webservices;
-import bioCycPlugin.webservices.ResultProperty;
import bioCycPlugin.model.Database;
import bioCycPlugin.model.Pathway;
+import bioCycPlugin.webservices.ResultProperty;
import bioCycPlugin.webservices.BioCycClient.FindPathwaysByTextParameters;
import bioCycPlugin.webservices.BioCycClient.GetPathwayParameters;
@@ -59,6 +59,7 @@
final BioCycClient client;
private CyLogger logger;
+ Database defaultDatabase = null;
JComboBox databaseCombo;
JTextField searchText;
JTable resultTable;
@@ -69,6 +70,8 @@
this.logger = logger;
databaseCombo = new JComboBox();
+ databaseCombo.addActionListener(this);
+ databaseCombo.setActionCommand(ACTION_SET_DATABASE);
resetDatabases();
searchText = new JTextField();
@@ -116,6 +119,9 @@
Object dbArray[] = databases.toArray();
Arrays.sort(dbArray);
databaseCombo.setModel(new DefaultComboBoxModel(dbArray));
+ defaultDatabase = Database.getDefaultDatabase(databases);
+ if (defaultDatabase != null)
+ databaseCombo.setSelectedItem(defaultDatabase);
}
public void actionPerformed(ActionEvent e) {
@@ -150,6 +156,9 @@
}
ex.printStackTrace();
}
+ } else if (ACTION_SET_DATABASE.equals(action)) {
+ defaultDatabase = (Database)
databaseCombo.getSelectedItem();
+ Database.setDefaultDatabase(defaultDatabase);
}
}
@@ -215,4 +224,5 @@
}
private static final String ACTION_SEARCH = "Search";
+ private static final String ACTION_SET_DATABASE = "Set Database";
}
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycRESTClient.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycRESTClient.java
2010-11-02 02:06:30 UTC (rev 22681)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycRESTClient.java
2010-11-02 18:38:23 UTC (rev 22682)
@@ -53,6 +53,7 @@
public class BioCycRESTClient {
CyLogger logger;
QueryHandler handler;
+ List<Database> databaseCache = null;
enum Operator {AND, OR};
@@ -70,7 +71,9 @@
}
public List<Database> listDatabases() {
- return Database.getDatabases(handler.query("dbs"));
+ if (databaseCache == null)
+ databaseCache =
Database.getDatabases(handler.query("dbs"));
+ return databaseCache;
}
public List<Pathway> findPathwaysByText(String query, String db) {
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