view xena_utils.py @ 20:3c735d06404b

Updated the xena jar to version 14

#!/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())