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1 #!/usr/bin/env python
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2 """
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3 xenaUtils: a set of python utilities for the Galaxy / Xena interface
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4 """
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5
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6 import os
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7 import socket
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8 import subprocess
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9
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10 def jarPath():
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11 """Return the full pathname of the xena jar file"""
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12 jarPath = os.getenv("XENA_JAR_PATH", "~")
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13 return(os.path.join(jarPath, "xena.jar"))
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14
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15
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16 def baseDir():
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17 return(os.getenv("XENA_BASE_DIR", "/tmp"))
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18
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19 def fileDir():
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20 return(baseDir() + "/files")
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21
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22 def isRunning(xenaPort):
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23 """Determine if Xena is running on the specified port"""
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24 query = "wget -q -O- http://localhost:%s/data/'(+ 1 2)'" % xenaPort
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25 try:
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26 result = subprocess.check_output(query, shell=True)
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27 except:
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28 return False
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29 else:
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30 return(result == "3.0")
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31
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32
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33 def findUnusedPort():
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34 """Find a random port that is available on the local system, and return
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35 the port number.
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36 """
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37 ss = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
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38 ss.bind(('', 0))
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39 portNumber = ss.getsockname()[1]
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40 ss.close()
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41 return(portNumber)
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42
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43 def isPortAvailable(port):
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44 """Test if a given port is available"""
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45 ss = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
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46 try:
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47 ss.bind(('', port))
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48 except:
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49 return False
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50 else:
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51 ss.close()
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52 return True
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53
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54
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55 def portFilename():
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56 """ Return the name of the file with the port of the running Xena,
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57 if any
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58 """
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59 xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
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60 xenaPortFilename = xenaBaseDir + "/xena.port"
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61 return(xenaPortFilename)
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62
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63
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64
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65
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66 def port(testIfAvailable=False, findNewPort=False):
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67 preferredXenaPort = 7220
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68 xenaPort = None
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69 xenaPortFname = portFilename()
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70 if os.path.exists(xenaPortFname):
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71 fp = open(xenaPortFname)
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72 line = fp.readline()
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73 xenaPort = int(line.rstrip())
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74 if testIfAvailable and not isRunning(xenaPort):
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75 # Xena is not running on the port. Make sure that
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76 # the port is not occupied by some other process
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77 if not isPortAvailable(xenaPort):
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78 #cmd = "lsof -t -i :%s -sTCP:LISTEN" % portID
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79 #pid = subprocess.check_output(cmd, shell=True).rstrip()
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80 #print "not available, used by",pid
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81 xenaPort = None
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82 if findNewPort and xenaPort == None:
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83 if isPortAvailable(preferredXenaPort):
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84 xenaPort = preferredXenaPort
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85 else:
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86 xenaPort = findUnusedPort()
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87 fp = open(portFilename(), "w")
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88 fp.write("%d\n" % xenaPort)
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89 fp.close()
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90 return(xenaPort)
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91
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92 def cleanUpPort():
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93 """ Clean up the port file after Xena has stopped running"""
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94 os.unlink(portFilename())
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95
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96
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97
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