Author: jm
Date: 2012-08-22 12:57:59 -0700 (Wed, 22 Aug 2012)
New Revision: 30250
Modified:
core3/gui-distribution/trunk/assembly/pom.xml
core3/gui-distribution/trunk/assembly/src/main/bin/cytoscape.bat
core3/gui-distribution/trunk/assembly/src/main/bin/cytoscape.sh
core3/gui-distribution/trunk/assembly/src/main/filtered-resources/etc/system.properties
core3/gui-distribution/trunk/assembly/src/main/resources/etc/org.ops4j.pax.logging.cfg
Log:
Fixes #1308: Cy3 no longer writes into its installation directory. All
metadata and logs are now stored in ~/CytoscapeConfiguration/3
Modified: core3/gui-distribution/trunk/assembly/pom.xml
===================================================================
--- core3/gui-distribution/trunk/assembly/pom.xml 2012-08-22 17:04:36 UTC
(rev 30249)
+++ core3/gui-distribution/trunk/assembly/pom.xml 2012-08-22 19:57:59 UTC
(rev 30250)
@@ -14,6 +14,10 @@
<packaging>pom</packaging>
<name>Cytoscape Karaf Distribution</name>
+ <properties>
+ <maven.resources.escapeString>\</maven.resources.escapeString>
+ </properties>
+
<dependencies>
<dependency>
<groupId>org.apache.karaf</groupId>
@@ -286,7 +290,11 @@
<token>MAIN=org.apache.karaf.main.Main</token>
<value>MAIN=org.cytoscape.launcher.internal.Launcher</value>
</replacement>
- </replacements>
+ <replacement>
+
<token>-Dkaraf.instances="${KARAF_BASE}/instances"</token>
+
<value>-Dkaraf.instances="${KARAF_DATA}/instances"</value>
+ </replacement>
+ </replacements>
</configuration>
</execution>
<execution>
@@ -305,6 +313,23 @@
<token>MAIN=org.apache.karaf.main.Main</token>
<value>MAIN=org.cytoscape.launcher.internal.Launcher</value>
</replacement>
+ <replacement>
+
<token>-Dkaraf.instances="%KARAF_HOME%\instances"</token>
+
<value>-Dkaraf.instances="%KARAF_DATA%\instances"</value>
+ </replacement>
+ <replacement>
+
<token>(__reg2.txt)</token>
+ <!--
Dirty hack: "%CD:~0,0%" expands to the empty string. That way, the
replacements below won't affect this one -->
+
<value>(%TEMP%\_%CD:~0,0%_reg2.txt)</value>
+ </replacement>
+ <replacement>
+
<token>__reg1.txt</token>
+
<value>"%TEMP%\__reg1.txt"</value>
+ </replacement>
+ <replacement>
+
<token>__reg2.txt</token>
+
<value>"%TEMP%\__reg2.txt"</value>
+ </replacement>
</replacements>
</configuration>
</execution>
Modified: core3/gui-distribution/trunk/assembly/src/main/bin/cytoscape.bat
===================================================================
--- core3/gui-distribution/trunk/assembly/src/main/bin/cytoscape.bat
2012-08-22 17:04:36 UTC (rev 30249)
+++ core3/gui-distribution/trunk/assembly/src/main/bin/cytoscape.bat
2012-08-22 19:57:59 UTC (rev 30250)
@@ -5,7 +5,7 @@
:: Create the Cytoscape.vmoptions file, if it doesn't exist.
IF EXIST "Cytoscape.vmoptions" GOTO vmoptionsFileExists
-CALL gen_vmoptions.bat
+CMD /C gen_vmoptions.bat
:vmoptionsFileExists
@@ -30,6 +30,9 @@
set PWD=%~dp0
set KARAF_OPTS=-Xss10M -Dcytoscape.home="%PWD:\=\\%" -Duser.dir="%PWD:\=\\%"
-splash:CytoscapeSplashScreen.png
+set KARAF_DATA="%USERPROFILE%\CytoscapeConfiguration\3\karaf_data"
+mkdir "%KARAF_DATA%\tmp"
+
if not "X%JAVA_HOME%"=="X" goto TryJDKEnd
goto :TryJRE
@@ -38,11 +41,11 @@
goto :EOF
:TryJRE
- reg export "HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Runtime Environment"
__reg1.txt
- if not exist __reg1.txt goto :TryJDK
- type __reg1.txt | find "CurrentVersion" > __reg2.txt
+ reg export "HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Runtime Environment"
%TEMP%\__reg1.txt
+ if not exist %TEMP%\__reg1.txt goto :TryJDK
+ type "%TEMP%\__reg1.txt" | find "CurrentVersion" > "%TEMP%\__reg2.txt"
if errorlevel 1 goto :TryJDK
- for /f "tokens=2 delims==" %%x in (__reg2.txt) do set JavaTemp=%%~x
+ for /f "tokens=2 delims==" %%x in ("%TEMP%\__reg2.txt") do set
JavaTemp=%%~x
if errorlevel 1 goto :TryJDK
set JavaTemp=%JavaTemp%##
set JavaTemp=%JavaTemp: ##=##%
@@ -51,29 +54,29 @@
set JavaTemp=%JavaTemp: ##=##%
set JavaTemp=%JavaTemp: ##=##%
set JavaTemp=%JavaTemp:##=%
- del __reg1.txt
- del __reg2.txt
- reg export "HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Runtime
Environment\%JavaTemp%" __reg1.txt
- if not exist __reg1.txt goto :TryJDK
- type __reg1.txt | find "JavaHome" > __reg2.txt
+ del "%TEMP%\__reg1.txt"
+ del "%TEMP%\__reg2.txt"
+ reg export "HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Runtime
Environment\%JavaTemp%" "%TEMP%\__reg1.txt"
+ if not exist "%TEMP%\__reg1.txt" goto :TryJDK
+ type "%TEMP%\__reg1.txt" | find "JavaHome" > "%TEMP%\__reg2.txt"
if errorlevel 1 goto :TryJDK
- for /f "tokens=2 delims==" %%x in (__reg2.txt) do set JAVA_HOME=%%~x
+ for /f "tokens=2 delims==" %%x in ("%TEMP%\__reg2.txt") do set
JAVA_HOME=%%~x
if errorlevel 1 goto :TryJDK
- del __reg1.txt
- del __reg2.txt
+ del "%TEMP%\__reg1.txt"
+ del "%TEMP%\__reg2.txt"
goto TryJDKEnd
:TryJDK
- reg export "HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Development Kit"
__reg1.txt
- if not exist __reg1.txt (
+ reg export "HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Development Kit"
"%TEMP%\__reg1.txt"
+ if not exist "%TEMP%\__reg1.txt" (
call :warn Unable to retrieve JAVA_HOME
goto END
)
- type __reg1.txt | find "CurrentVersion" > __reg2.txt
+ type "%TEMP%\__reg1.txt" | find "CurrentVersion" > "%TEMP%\__reg2.txt"
if errorlevel 1 (
call :warn Unable to retrieve JAVA_HOME
goto END
)
- for /f "tokens=2 delims==" %%x in (__reg2.txt) do set JavaTemp=%%~x
+ for /f "tokens=2 delims==" %%x in ("%TEMP%\__reg2.txt") do set
JavaTemp=%%~x
if errorlevel 1 (
call :warn Unable to retrieve JAVA_HOME
goto END
@@ -85,25 +88,25 @@
set JavaTemp=%JavaTemp: ##=##%
set JavaTemp=%JavaTemp: ##=##%
set JavaTemp=%JavaTemp:##=%
- del __reg1.txt
- del __reg2.txt
- reg export "HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Development
Kit\%JavaTemp%" __reg1.txt
- if not exist __reg1.txt (
+ del "%TEMP%\__reg1.txt"
+ del "%TEMP%\__reg2.txt"
+ reg export "HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Development
Kit\%JavaTemp%" "%TEMP%\__reg1.txt"
+ if not exist "%TEMP%\__reg1.txt" (
call :warn Unable to retrieve JAVA_HOME from JDK
goto END
)
- type __reg1.txt | find "JavaHome" > __reg2.txt
+ type "%TEMP%\__reg1.txt" | find "JavaHome" > "%TEMP%\__reg2.txt"
if errorlevel 1 (
call :warn Unable to retrieve JAVA_HOME
goto END
)
- for /f "tokens=2 delims==" %%x in (__reg2.txt) do set JAVA_HOME=%%~x
+ for /f "tokens=2 delims==" %%x in ("%TEMP%\__reg2.txt") do set
JAVA_HOME=%%~x
if errorlevel 1 (
call :warn Unable to retrieve JAVA_HOME
goto END
)
- del __reg1.txt
- del __reg2.txt
+ del "%TEMP%\__reg1.txt"
+ del "%TEMP%\__reg2.txt"
:TryJDKEnd
if not exist "%JAVA_HOME%" (
call :warn JAVA_HOME is not valid: "%JAVA_HOME%"
Modified: core3/gui-distribution/trunk/assembly/src/main/bin/cytoscape.sh
===================================================================
--- core3/gui-distribution/trunk/assembly/src/main/bin/cytoscape.sh
2012-08-22 17:04:36 UTC (rev 30249)
+++ core3/gui-distribution/trunk/assembly/src/main/bin/cytoscape.sh
2012-08-22 19:57:59 UTC (rev 30250)
@@ -45,4 +45,7 @@
# working directory to framework is not known.
export KARAF_OPTS=-Xss10M\ -Duser.dir="$PWD"\
-Dcytoscape.home="$CYTOSCAPE_HOME_ABS"\ -splash:CytoscapeSplashScreen.png\
"$CYTOSCAPE_MAC_OPTS"
+export KARAF_DATA="${HOME}/CytoscapeConfiguration/3/karaf_data"
+mkdir -p "${KARAF_DATA}/tmp"
+
$script_path/framework/bin/karaf "$@"
Modified:
core3/gui-distribution/trunk/assembly/src/main/filtered-resources/etc/system.properties
===================================================================
---
core3/gui-distribution/trunk/assembly/src/main/filtered-resources/etc/system.properties
2012-08-22 17:04:36 UTC (rev 30249)
+++
core3/gui-distribution/trunk/assembly/src/main/filtered-resources/etc/system.properties
2012-08-22 19:57:59 UTC (rev 30250)
@@ -8,3 +8,5 @@
apple.awt.rendering=speed
apple.awt.fileDialogForDirectories=true
com.apple.mrj.application.apple.menu.about.name=Cytoscape
+
+karaf.lock.dir=\${user.home}/CytoscapeConfiguration/3
Modified:
core3/gui-distribution/trunk/assembly/src/main/resources/etc/org.ops4j.pax.logging.cfg
===================================================================
---
core3/gui-distribution/trunk/assembly/src/main/resources/etc/org.ops4j.pax.logging.cfg
2012-08-22 17:04:36 UTC (rev 30249)
+++
core3/gui-distribution/trunk/assembly/src/main/resources/etc/org.ops4j.pax.logging.cfg
2012-08-22 19:57:59 UTC (rev 30250)
@@ -20,7 +20,7 @@
log4j.appender.file=org.apache.log4j.DailyRollingFileAppender
log4j.appender.file.threshold=INFO
-log4j.appender.file.File=framework-cytoscape.log
+log4j.appender.file.File=${user.home}/CytoscapeConfiguration/3/framework-cytoscape.log
log4j.appender.file.layout=org.apache.log4j.PatternLayout
log4j.appender.file.layout.ConversionPattern=%d [%t] %-5p %c - %m%n
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