# HG changeset patch
# User melissacline
# Date 1409868212 25200
# Node ID 00ea1bdc1aed55d69f74a4a10d31772b2c1f465c
# Parent  0676a227dbc6f22c039384b20b308ef91a568c0c
Updated the repo in the test toolshed - this should work now

diff -r 0676a227dbc6 -r 00ea1bdc1aed startXena.py
--- a/startXena.py	Wed Sep 03 15:37:49 2014 -0400
+++ b/startXena.py	Thu Sep 04 15:03:32 2014 -0700
@@ -5,15 +5,15 @@
 import subprocess
 import sys
 
-def stop_err(msg, fp, error_level=1):
+def stop_err(msg, error_level=1):
    """Print error message to stdout and quit with given error level."""
-   #sys.stderr.write("%s\n" % msg)
-   fp.write("%s\n" % msg)
-   fp.write("error code %d\n" % error_level)
+   sys.stderr.write("%s\n" % msg)
+   #fp.write("%s\n" % msg)
+   #fp.write("error code %d\n" % error_level)
    sys.exit(error_level)
 
     
-def run(cmd, fp):
+def run(cmd):
     #Avoid using shell=True when we call subprocess to ensure if the Python
     #script is killed, so too is the child process.
     try:
@@ -26,27 +26,32 @@
     return_code = child.returncode
     if return_code:
         if stderr and stdout:
-            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr), fp)
+            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr))
         else:
-            stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr), fp)
+            stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr))
 
 
 
 def main():
-    jarPath = os.getenv("JAVA_JAR_PATH", "~")
-    xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
-    xenaJarPath = os.path.join(jarPath, "xena.jar")
-    xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
-    cmdline = "java -jar %s -r %s/xena/files -d %s/xena/db -t %s/xena/tmp" % (xenaJarPath, xenaBaseDir, xenaBaseDir, xenaBaseDir)
-    for ii in range(1,len(sys.argv)):
-        cmdline = "%s %s" % (cmdline, sys.argv[ii])
-    print "executing", cmdline
-    fp = open("/inside/home/cline/tmp/xena.out", "w")
-    fp.write("jar path (not paht) %s\n" % (jarPath))
-    fp.write("xena base dir %s\n" % (xenaBaseDir))
-    fp.write(cmdline)
-    run(cmdline, fp)
-    fp.close()
+   #parser = argparse.ArgumentParser()
+   #parser.add_argument("-H", "--host", type=str)
+   #parser.add_argument("-p", "--port", type=str)
+   #args = parser.parse_args()
+
+   jarPath = os.getenv("JAVA_JAR_PATH", "~")
+   xenaJarPath = os.path.join(jarPath, "xena.jar")
+   xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
+   #xenaBaseDir = os.getenv("__tool_data_path__", "~") + "/shared/xena"
+   #xenaBaseDir = args.toolDataPath + "/shared/xena"
+   cmdline = "java -jar %s -r %s/files -d %s/xena/db -t %s/tmp" % (xenaJarPath, xenaBaseDir, xenaBaseDir, xenaBaseDir)
+   for ii in range(1,len(sys.argv)):
+       cmdline = "%s %s" % (cmdline, sys.argv[ii])
+   fp = open("/Users/melissacline/tmp/xena.out", "w")
+   fp.write("jar path (not paht) %s\n" % (jarPath))
+   fp.write("xena base dir %s\n" % (xenaBaseDir))
+   fp.write(cmdline)
+   run(cmdline)
+   fp.close()
 
 if __name__ == '__main__':
     main( )
diff -r 0676a227dbc6 -r 00ea1bdc1aed tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 03 15:37:49 2014 -0400
+++ b/tool_dependencies.xml	Thu Sep 04 15:03:32 2014 -0700
@@ -3,16 +3,16 @@
   <package name="installXena" version="1.0">
     <install version="1.0">
       <actions>
+	<action type="set_environment">
+          <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+        </action>  
+	<action type="set_environment">
+          <environment_variable name="XENA_BASE_DIR" action="set_to">$INSTALL_DIR</environment_variable>
+        </action>
 	<action type="move_file">
 	  <source>${REPOSITORY_INSTALL_DIR}/xena/xena.jar</source>
 	  <destination>${INSTALL_DIR}</destination>
 	</action>
-	<action type="set_environment">
-          <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-        </action>  
-	<action type="set_environment">
-          <environment_variable name="XENA_BASE_DIR" action="set_to">$INSTALL_DIR/xena</environment_variable>
-        </action>
       </actions>
     </install>
   </package>
diff -r 0676a227dbc6 -r 00ea1bdc1aed xena.xml
--- a/xena.xml	Wed Sep 03 15:37:49 2014 -0400
+++ b/xena.xml	Thu Sep 04 15:03:32 2014 -0700
@@ -4,7 +4,7 @@
    <requirement type="package" version="1.0">installXena</requirement>
  </requirements>
   <command interpreter="python">
-    startXena.py  -H 0.0.0.0 -p 1236 &amp;
+    startXena.py   -H 0.0.0.0 -p 1236 &amp;
   </command>
  <help>
     Press the Execute button to start the Xena VM.