Author: rozagh
Date: 2012-08-20 10:34:44 -0700 (Mon, 20 Aug 2012)
New Revision: 30228
Modified:
core3/api/trunk/property-api/src/main/java/org/cytoscape/property/CyProperty.java
core3/gui-distribution/trunk/assembly/pom.xml
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java
core3/impl/trunk/application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationConfigurationImpl.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterApp.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/Plugin.java
Log:
fixes #1310 The ./cytoscape directory is renamed to CytoscapeConfiguration and
3.0 directory is replaced with 3. The hierarchical structure of having minor
version numbers under major version number (e.g. CytoscapeConfigiration/3/0.1/
) is pending for a decision to be made.
Modified:
core3/api/trunk/property-api/src/main/java/org/cytoscape/property/CyProperty.java
===================================================================
---
core3/api/trunk/property-api/src/main/java/org/cytoscape/property/CyProperty.java
2012-08-20 17:18:52 UTC (rev 30227)
+++
core3/api/trunk/property-api/src/main/java/org/cytoscape/property/CyProperty.java
2012-08-20 17:34:44 UTC (rev 30228)
@@ -50,7 +50,7 @@
* will be a subdirectory of the "user.home" directory defined in the
default Java
* system properties ({@link System#getProperties()}).
*/
- String DEFAULT_PROPS_CONFIG_DIR = ".cytoscape";
+ String DEFAULT_PROPS_CONFIG_DIR = "CytoscapeConfiguration";
/**
* Returns the name of the CyProperty.
Modified: core3/gui-distribution/trunk/assembly/pom.xml
===================================================================
--- core3/gui-distribution/trunk/assembly/pom.xml 2012-08-20 17:18:52 UTC
(rev 30227)
+++ core3/gui-distribution/trunk/assembly/pom.xml 2012-08-20 17:34:44 UTC
(rev 30228)
@@ -318,7 +318,7 @@
<file>target/cytoscape/framework/etc/org.apache.felix.fileinstall-deploy.cfg</file>
<unescape>false</unescape>
<token>felix.fileinstall.dir.*</token>
-
<value>felix.fileinstall.dir =
\$\{user.home\}/.cytoscape/3.0/apps/installed</value>
+
<value>felix.fileinstall.dir =
\$\{user.home\}/CytoscapeConfiguration/3/apps/installed</value>
</configuration>
</execution>
</executions>
Modified:
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java
===================================================================
---
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java
2012-08-20 17:18:52 UTC (rev 30227)
+++
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java
2012-08-20 17:34:44 UTC (rev 30228)
@@ -70,7 +70,7 @@
/** This subdirectory in the local Cytoscape storage directory is used
to store app data, as
* well as installed and uninstalled apps. */
- private static final String APPS_DIRECTORY_NAME = "3.0" +
File.separator + "apps";
+ private static final String APPS_DIRECTORY_NAME = "3" + File.separator
+ "apps";
/** The set of all apps, represented by {@link App} objects, registered
to this App Manager. */
private Set<App> apps;
Modified:
core3/impl/trunk/application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationConfigurationImpl.java
===================================================================
---
core3/impl/trunk/application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationConfigurationImpl.java
2012-08-20 17:18:52 UTC (rev 30227)
+++
core3/impl/trunk/application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationConfigurationImpl.java
2012-08-20 17:34:44 UTC (rev 30228)
@@ -4,6 +4,7 @@
import java.util.Dictionary;
import org.cytoscape.application.CyApplicationConfiguration;
+import org.cytoscape.property.CyProperty;
import org.osgi.framework.Bundle;
import org.osgi.framework.FrameworkUtil;
import org.slf4j.Logger;
@@ -12,7 +13,7 @@
public class CyApplicationConfigurationImpl implements
CyApplicationConfiguration {
/** Default configuration directory used for all Cytoscape
configuration files */
- public static final String DEFAULT_CONFIG_DIR = ".cytoscape";
+ public static final String DEFAULT_CONFIG_DIR =
CyProperty.DEFAULT_PROPS_CONFIG_DIR ;
private static final Logger logger =
LoggerFactory.getLogger(CyApplicationConfigurationImpl.class);
@@ -29,7 +30,7 @@
if(configFileLocation.exists() == false) {
configFileLocation.mkdir();
- logger.warn(".cytoscape directory was not available.
New directory created.");
+ logger.warn("CytoscapeConfiguration directory was not
available. New directory created.");
} else {
logger.info("Setting file directory = " +
configFileLocation.getAbsolutePath());
}
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterApp.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterApp.java
2012-08-20 17:18:52 UTC (rev 30227)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterApp.java
2012-08-20 17:34:44 UTC (rev 30228)
@@ -188,7 +188,7 @@
InputStream is = null;
try {
- // Load global filters from ".cytoscape" directory.
+ // Load global filters from
CyProperty.DEFAULT_PROPS_CONFIG_DIR directory.
final File file = getGlobalFilterFile();
if (file.exists()) {
@@ -234,7 +234,7 @@
globalFilters.add(cf);
}
- // Save global filters in the ".cytoscape" directory
+ // Save global filters in the
CyProperty.DEFAULT_PROPS_CONFIG_DIR directory
final File file = getGlobalFilterFile();
writer.saveGlobalPropFile(globalFilters, file);
}
@@ -242,8 +242,8 @@
private File getGlobalFilterFile() {
String cyConfigVerDir = new File(
ServicesUtil.cyApplicationConfigurationServiceRef.getConfigurationDirectoryLocation(),
- File.separator +
ServicesUtil.cytoscapeVersionService.getMajorVersion() + "."
- +
ServicesUtil.cytoscapeVersionService.getMinorVersion()).getAbsolutePath();
+ File.separator +
ServicesUtil.cytoscapeVersionService.getMajorVersion()).getAbsolutePath(); // +
"."
+ //+
ServicesUtil.cytoscapeVersionService.getMinorVersion()).getAbsolutePath();
final File file = new File(cyConfigVerDir + File.separator +
FilterUtil.DEFAULT_FILE_NAME);
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/Plugin.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/Plugin.java
2012-08-20 17:18:52 UTC (rev 30227)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/Plugin.java
2012-08-20 17:34:44 UTC (rev 30228)
@@ -31,6 +31,7 @@
import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
import org.cytoscape.application.CyVersion;
+import org.cytoscape.property.CyProperty;
/**
@@ -45,7 +46,7 @@
/**
* Name of directory that contains Cytoscape plugins as a path relative
to Cytoscape's root directory.
*/
- public static final String cytoscapeDir =
System.getProperty("user.home") + File.separator + ".cytoscape";
+ public static final String cytoscapeDir =
System.getProperty("user.home") + File.separator +
CyProperty.DEFAULT_PROPS_CONFIG_DIR ;
/**
* Name of XML settings file. Both the internal and external setting
files have this name.
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