Author: scooter
Date: 2010-11-11 11:21:08 -0800 (Thu, 11 Nov 2010)
New Revision: 22820
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/BioCycPlugin.java
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClient.java
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClientGui.java
Log:
Added support for multiple sites.
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/BioCycPlugin.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/BioCycPlugin.java
2010-11-11 00:14:33 UTC (rev 22819)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/BioCycPlugin.java
2010-11-11 19:21:08 UTC (rev 22820)
@@ -55,9 +55,9 @@
private BioCycClient wpclient;
private static Properties defaultProps = null;
- protected static final String WEBSERVICE_URL = "biocyc.webservice.uri";
+ public static final String WEBSERVICE_URL = "biocyc.webservice.uri";
// protected static final String DEFAULT_URL =
"http://brg-preview.ai.sri.com/";;
- protected static final String DEFAULT_URL = "http://websvc.biocyc.org/";;
+ public static final String DEFAULT_URL = "http://websvc.biocyc.org/";;
/**
* We don't do much at initialization time
@@ -75,12 +75,6 @@
// 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();
@@ -113,7 +107,12 @@
}
public static String getBaseUrl() {
- return
CytoscapeInit.getProperties().getProperty(WEBSERVICE_URL);
+ String url = defaultProps.getProperty(WEBSERVICE_URL);
+ if (url == null) {
+ url = DEFAULT_URL;
+ setProp(WEBSERVICE_URL, DEFAULT_URL);
+ }
+ return url;
}
public void propertyChange(PropertyChangeEvent evt) {
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClient.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClient.java
2010-11-11 00:14:33 UTC (rev 22819)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClient.java
2010-11-11 19:21:08 UTC (rev 22820)
@@ -100,6 +100,14 @@
return stub;
}
+ public String getDescription() {
+ String description = "<html><body><b>BioCyc</b> is one of
several repositories using the Pathway Tools software (";
+ description += "<a
href=\"http://bioinformatics.ai.sri.com/ptools\";>http://bioinformatics.ai.sri.com/ptools</a>)
";
+ description += "for pathway information on a variety of
species. This plugin supports any of the repositories ";
+ description += "running Pathway Tools release <b>14.5</b> or
later</body></html>";
+ return description;
+ }
+
/**
* Check if a working connection to the wikipathways
* web service is available.
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClientGui.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClientGui.java
2010-11-11 00:14:33 UTC (rev 22819)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/webservices/BioCycClientGui.java
2010-11-11 19:21:08 UTC (rev 22820)
@@ -16,6 +16,7 @@
//
package bioCycPlugin.webservices;
+import bioCycPlugin.BioCycPlugin;
import bioCycPlugin.model.Database;
import bioCycPlugin.model.Pathway;
import bioCycPlugin.webservices.ResultProperty;
@@ -62,6 +63,7 @@
Database defaultDatabase = null;
JComboBox databaseCombo;
JTextField searchText;
+ JTextField webServiceText;
JTable resultTable;
ListWithPropertiesTableModel<ResultProperty, ResultRow> tableModel;
@@ -78,6 +80,11 @@
searchText.setActionCommand(ACTION_SEARCH);
searchText.addActionListener(this);
+ webServiceText = new JTextField();
+ webServiceText.setActionCommand(ACTION_SET_WEBSERVICE);
+ webServiceText.addActionListener(this);
+ webServiceText.setText(BioCycPlugin.getBaseUrl());
+
JButton searchBtn = new JButton("Search");
searchBtn.setActionCommand(ACTION_SEARCH);
searchBtn.addActionListener(this);
@@ -96,15 +103,17 @@
setLayout(new FormLayout(
"4dlu, pref, 2dlu, fill:pref:grow, 4dlu, pref,
4dlu, pref, 4dlu",
- "4dlu, pref, 4dlu, pref, 4dlu, fill:pref:grow,
4dlu"
+ "4dlu, pref, 4dlu, pref, 4dlu, pref, 4dlu,
fill:pref:grow, 4dlu"
));
CellConstraints cc = new CellConstraints();
- add(new JLabel("Database:"), cc.xy(2, 2));
- add(databaseCombo, cc.xy(4, 2));
- add(new JLabel("Search:"), cc.xy(2, 4));
- add(searchText, cc.xy(4, 4));
- add(searchBtn, cc.xy(8, 4));
- add(new JScrollPane(resultTable), cc.xyw(2, 6, 7));
+ add(new JLabel("Web Server:"), cc.xy(2, 2));
+ add(webServiceText, cc.xy(4, 2));
+ add(new JLabel("Database:"), cc.xy(2, 4));
+ add(databaseCombo, cc.xy(4, 4));
+ add(new JLabel("Search:"), cc.xy(2, 6));
+ add(searchText, cc.xy(4, 6));
+ add(searchBtn, cc.xy(8, 6));
+ add(new JScrollPane(resultTable), cc.xyw(2, 8, 7));
}
protected void resetDatabases() {
@@ -159,6 +168,15 @@
} else if (ACTION_SET_DATABASE.equals(action)) {
defaultDatabase = (Database)
databaseCombo.getSelectedItem();
Database.setDefaultDatabase(defaultDatabase);
+ } else if (ACTION_SET_WEBSERVICE.equals(action)) {
+ String url = webServiceText.getText();
+ if (url == null || url.length() == 0)
+ url = BioCycPlugin.DEFAULT_URL;
+ BioCycPlugin.setProp(BioCycPlugin.WEBSERVICE_URL, url);
+ client.getStub();
+ // Now, update the text again
+ webServiceText.setText(url);
+ resetDatabases();
}
}
@@ -225,4 +243,5 @@
private static final String ACTION_SEARCH = "Search";
private static final String ACTION_SET_DATABASE = "Set Database";
+ private static final String ACTION_SET_WEBSERVICE = "Set Web Service
URL";
}
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