diff xena_utils.py @ 0:8bb037f88ed2

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xena_utils.py	Tue Jan 13 23:37:23 2015 -0500
@@ -0,0 +1,97 @@
+#!/usr/bin/env python
+""" 
+xenaUtils: a set of python utilities for the Galaxy / Xena interface
+"""
+
+import os
+import socket
+import subprocess
+
+def jarPath():
+    """Return the full pathname of the xena jar file"""
+    jarPath = os.getenv("XENA_JAR_PATH", "~")
+    return(os.path.join(jarPath, "xena.jar"))
+
+
+def baseDir():
+    return(os.getenv("XENA_BASE_DIR", "/tmp"))
+
+def fileDir():
+    return(baseDir() + "/files")
+
+def isRunning(xenaPort):
+    """Determine if Xena is running on the specified port"""
+    query = "wget -q -O- http://localhost:%s/data/'(+ 1 2)'" % xenaPort
+    try:
+        result = subprocess.check_output(query, shell=True)
+    except:
+        return False
+    else:
+        return(result == "3.0")
+    
+
+def findUnusedPort():
+    """Find a random port that is available on the local system, and return
+    the port number.
+    """
+    ss = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+    ss.bind(('', 0))
+    portNumber = ss.getsockname()[1]
+    ss.close()
+    return(portNumber)
+
+def isPortAvailable(port):
+    """Test if a given port is available"""
+    ss = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+    try:
+        ss.bind(('', port))
+    except:
+        return False
+    else:
+        ss.close()
+        return True
+
+
+def portFilename():
+    """ Return the name of the file with the port of the running Xena, 
+    if any
+    """
+    xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
+    xenaPortFilename = xenaBaseDir + "/xena.port"
+    return(xenaPortFilename)
+
+
+
+
+def port(testIfAvailable=False, findNewPort=False):
+    preferredXenaPort = 7220
+    xenaPort = None
+    xenaPortFname = portFilename()
+    if os.path.exists(xenaPortFname):
+        fp = open(xenaPortFname)
+        line = fp.readline()
+        xenaPort = int(line.rstrip())
+        if testIfAvailable and not isRunning(xenaPort):
+            # Xena is not running on the port.  Make sure that
+            # the port is not occupied by some other process
+            if not isPortAvailable(xenaPort):
+                #cmd = "lsof -t -i :%s -sTCP:LISTEN" % portID
+                #pid = subprocess.check_output(cmd, shell=True).rstrip()
+                #print "not available, used by",pid
+                xenaPort = None
+    if findNewPort and xenaPort == None:
+        if isPortAvailable(preferredXenaPort):
+            xenaPort = preferredXenaPort
+        else:
+            xenaPort = findUnusedPort()
+        fp = open(portFilename(), "w")
+        fp.write("%d\n" % xenaPort)
+        fp.close()
+    return(xenaPort)
+
+def cleanUpPort():
+    """ Clean up the port file after Xena has stopped running"""
+    os.unlink(portFilename())
+
+
+