Author: scooter
Date: 2010-12-21 11:33:44 -0800 (Tue, 21 Dec 2010)
New Revision: 23256
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/build.xml
csplugins/trunk/ucsf/scooter/bioCycPlugin/resources/plugin.props
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/commands/BioCycCommandHandler.java
Log:
Added new command to switch repositories
Modified: csplugins/trunk/ucsf/scooter/bioCycPlugin/build.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/bioCycPlugin/build.xml 2010-12-21 01:57:49 UTC
(rev 23255)
+++ csplugins/trunk/ucsf/scooter/bioCycPlugin/build.xml 2010-12-21 19:33:44 UTC
(rev 23256)
@@ -23,7 +23,7 @@
<!-- The version of your plugin. To support plugin.props, make sure the
version is expressed in decimal notation, e.g. 3.0, 3.1, 3.14, etc.
-->
- <property name="version" value="0.9"/>
+ <property name="version" value="0.91"/>
<!-- The version of Cytoscape that you depend on. -->
<property name="cytoscape.version" value="2.8.0"/>
Modified: csplugins/trunk/ucsf/scooter/bioCycPlugin/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/bioCycPlugin/resources/plugin.props
2010-12-21 01:57:49 UTC (rev 23255)
+++ csplugins/trunk/ucsf/scooter/bioCycPlugin/resources/plugin.props
2010-12-21 19:33:44 UTC (rev 23256)
@@ -13,7 +13,7 @@
pluginDescription=This plugin provides a web services interface to Pathway
Tools repositories
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.9
+pluginVersion=0.91
# Compatible Cytoscape version
cytoscapeVersion=2.8
Modified:
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/commands/BioCycCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/commands/BioCycCommandHandler.java
2010-12-21 01:57:49 UTC (rev 23255)
+++
csplugins/trunk/ucsf/scooter/bioCycPlugin/src/bioCycPlugin/commands/BioCycCommandHandler.java
2010-12-21 19:33:44 UTC (rev 23256)
@@ -47,6 +47,7 @@
import cytoscape.layout.Tunable;
import cytoscape.logger.CyLogger;
+import bioCycPlugin.BioCycPlugin;
import bioCycPlugin.model.Database;
import bioCycPlugin.model.Gene;
import bioCycPlugin.model.Pathway;
@@ -55,7 +56,7 @@
enum Command {
LISTDATABASES("list databases",
- "List all of the available databases", ""),
+ "List all of the available databases", null),
LISTGENES("list genes",
"List all of the genes that meet the criteria",
"database=ecoli|name"),
@@ -70,7 +71,10 @@
"database=ecoli|protein|gene"),
LOADPATHWAY("load pathway",
"Load a pathway in biopax format",
- "database=ecoli|pathway");
+ "database=ecoli|pathway"),
+ OPENRESOURCE("open resource",
+ "Open a Pathway Tools Resource",
+ "url");
private String command = null;
private String argList = null;
@@ -104,6 +108,7 @@
public static final String PROTEIN = "protein";
public static final String REACTION = "reaction";
public static final String SUBSTRATE = "substrate";
+ public static final String URL = "url";
public BioCycCommandHandler(String namespace, CyLogger logger) {
super(CyCommandManager.reserveNamespace(namespace));
@@ -139,11 +144,28 @@
return result;
}
+ // OPENRESOURCE("open resource",
+ // "Open a Pathway Tools Resource",
+ // "url");
+ if (Command.OPENRESOURCE.equals(command)) {
+ String url = getArg(command, URL, args);
+ if (url == null || url.length() == 0)
+ throw new CyCommandException("Must specify a
url for the resource");
+
+ String oldUrl = BioCycPlugin.getBaseUrl();
+ BioCycPlugin.setProp(BioCycPlugin.WEBSERVICE_URL, url);
+ result.addMessage("Switched resource from "+oldUrl+" to
"+url);
+ return result;
+ }
+
// All of the rest of these require a database
String database = getArg(command, DATABASE, args);
if (database == null)
throw new CyCommandException("Must specify a database");
+ // Databases are upper-case
+ database = database.toUpperCase();
+
// LOADPATHWAY("load pathway",
// "Load a pathway in biopax format",
// "database=ecoli|pathway");
--
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