Author: scooter
Date: 2009-03-16 11:25:45 -0700 (Mon, 16 Mar 2009)
New Revision: 16286
Modified:
csplugins/trunk/ucsf/scooter/batchTool/examples/test.com
csplugins/trunk/ucsf/scooter/batchTool/resources/plugin.props
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/BatchTool.java
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/AbstractCommand.java
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/ExportCommand.java
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/LayoutCommand.java
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/SaveCommand.java
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/SetCommand.java
Log:
Updated to move the toLowerCase functionality and fix a bug in Set
Modified: csplugins/trunk/ucsf/scooter/batchTool/examples/test.com
===================================================================
--- csplugins/trunk/ucsf/scooter/batchTool/examples/test.com 2009-03-16
18:00:48 UTC (rev 16285)
+++ csplugins/trunk/ucsf/scooter/batchTool/examples/test.com 2009-03-16
18:25:45 UTC (rev 16286)
@@ -1,6 +1,7 @@
import network pte.xgmml
import node attributes subgroup.noa
layout force-directed
-export network as pdf to /Users/scooter/Desktop/test.pdf zoom=10
+set exportTextAsShape=false cytoscape.version.number=2.6.2
+export network as pdf to /home/scooter/Desktop/test.pdf zoom=10
exit
Modified: csplugins/trunk/ucsf/scooter/batchTool/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/batchTool/resources/plugin.props
2009-03-16 18:00:48 UTC (rev 16285)
+++ csplugins/trunk/ucsf/scooter/batchTool/resources/plugin.props
2009-03-16 18:25:45 UTC (rev 16286)
@@ -13,10 +13,10 @@
pluginDescription=This plugin provides a simple proof-of-concept scripting
capability for Cytoscape
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.5
+pluginVersion=1.1
# Compatible Cytoscape version
-cytoscapeVersion=2.6
+cytoscapeVersion=2.6.1,2.6.2
# Category, use one of the categories listed on the website or create your own
pluginCategory=Other
@@ -31,4 +31,4 @@
pluginAuthorsIntsitutions=John "Scooter" Morris:UCSF
# Date this plugin/plugin version was released
-releaseDate=March 18, 2008
+releaseDate=March 16, 2009
Modified: csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/BatchTool.java
===================================================================
--- csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/BatchTool.java
2009-03-16 18:00:48 UTC (rev 16285)
+++ csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/BatchTool.java
2009-03-16 18:25:45 UTC (rev 16286)
@@ -163,7 +163,7 @@
optMap.put(key, str);
inPair = false;
} else {
- args.add(str.toLowerCase());
+ args.add(str);
}
tokenStart = i+1;
@@ -173,7 +173,7 @@
if (inQuote) continue;
if (i > tokenStart+1) {
str = input.substring(tokenStart, i);
- args.add(str.toLowerCase());
+ args.add(str);
i = input.length();
}
break;
@@ -201,7 +201,7 @@
*/
if (args.size() > 0)
- return args.get(0);
+ return args.get(0).toLowerCase();
return null;
}
Modified:
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/AbstractCommand.java
===================================================================
---
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/AbstractCommand.java
2009-03-16 18:00:48 UTC (rev 16285)
+++
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/AbstractCommand.java
2009-03-16 18:25:45 UTC (rev 16286)
@@ -75,7 +75,7 @@
*/
public boolean commpare(String command, String userInput, int minInput)
{
if (userInput.length() < minInput) return false;
- return command.startsWith(userInput);
+ return command.toLowerCase().startsWith(userInput);
}
}
Modified:
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/ExportCommand.java
===================================================================
---
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/ExportCommand.java
2009-03-16 18:00:48 UTC (rev 16285)
+++
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/ExportCommand.java
2009-03-16 18:25:45 UTC (rev 16286)
@@ -119,7 +119,7 @@
CyLogger.getLogger(ExportCommand.class).debug("parsing");
// Get the rest of the information.
- if (obj.equals("network")) {
+ if (obj.toLowerCase().equals("network")) {
object = ExportObject.NETWORK;
// Get our "as" clause
@@ -130,17 +130,17 @@
if (fileName == null)
throw new ParseException("export network
requires a file name");
- } else if (obj.equals("node")) {
+ } else if (obj.toLowerCase().equals("node")) {
object = ExportObject.NODEATTR;
if (!("attributes".startsWith(args.get(2)))) {
throw new ParseException("Don't know how to
export node "+args.get(2));
}
- } else if (obj.equals("edge")) {
+ } else if (obj.toLowerCase().equals("edge")) {
object = ExportObject.EDGEATTR;
if (!("attributes".startsWith(args.get(2)))) {
throw new ParseException("Don't know how to
export edge "+args.get(2));
}
- } else if (obj.equals("vizmap")) {
+ } else if (obj.toLowerCase().equals("vizmap")) {
object = ExportObject.VIZMAP;
}
Modified:
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/LayoutCommand.java
===================================================================
---
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/LayoutCommand.java
2009-03-16 18:00:48 UTC (rev 16285)
+++
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/LayoutCommand.java
2009-03-16 18:25:45 UTC (rev 16286)
@@ -80,7 +80,7 @@
// Second argument must be a registered layout
layoutName = args.get(1);
CyLogger.getLogger(LayoutCommand.class).debug("Layout type:
"+layoutName);
- layoutAlgorithm = CyLayouts.getLayout(layoutName);
+ layoutAlgorithm = CyLayouts.getLayout(layoutName.toLowerCase());
if (layoutAlgorithm == null) {
throw new ParseException("The layout "+args.get(1)+"
isn't available");
}
Modified:
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/SaveCommand.java
===================================================================
---
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/SaveCommand.java
2009-03-16 18:00:48 UTC (rev 16285)
+++
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/SaveCommand.java
2009-03-16 18:25:45 UTC (rev 16286)
@@ -71,7 +71,7 @@
*/
public int parse(List<String> args, HashMap<String,String>optMap)
throws ParseException {
// Second argument must be a registered layout
- if (args.get(1).equals("as")) {
+ if (args.get(1).toLowerCase().equals("as")) {
fileName = args.get(2);
} else {
fileName = Cytoscape.getCurrentSessionFileName();
Modified:
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/SetCommand.java
===================================================================
---
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/SetCommand.java
2009-03-16 18:00:48 UTC (rev 16285)
+++
csplugins/trunk/ucsf/scooter/batchTool/src/batchTool/commands/SetCommand.java
2009-03-16 18:25:45 UTC (rev 16286)
@@ -71,7 +71,7 @@
* set exportTextAsShape=true
*/
public int parse(List<String> args, HashMap<String,String>optMap)
throws ParseException {
- if (args.size() < 2)
+ if (optMap.size() < 1)
throw new ParseException("Nothing to set");
// Get the properties
Properties props = CytoscapeInit.getProperties();
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