Mercurial > repos > melissacline > ucsc_xena_platform
annotate runXena.py @ 31:bb84d3bc5308
make Xena VM already running on ... message more useful for adding the data hub
| author | jingchunzhu <jingchunzhu@gmail.com> |
|---|---|
| date | Tue, 21 Jul 2015 21:09:37 -0700 |
| parents | 77f5d8cbac77 |
| children | 63b1ba1e3424 |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 # To kick off the script, run the following from the python directory: | |
| 3 # PYTHONPATH=`pwd` python testdaemon.py start | |
| 4 | |
| 5 #standard python libs | |
| 6 import logging | |
| 7 import os | |
| 8 import signal | |
|
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77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
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diff
changeset
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9 import subprocess, shlex |
| 0 | 10 import sys |
| 11 import time | |
| 12 import traceback | |
| 13 import xena_utils as xena | |
| 14 | |
| 15 #third party libs | |
| 16 from daemon import runner | |
| 17 from lockfile import LockTimeout | |
| 18 | |
| 19 | |
| 20 class App(): | |
| 21 | |
| 22 def __init__(self): | |
| 23 xenaBaseDir = xena.baseDir() | |
| 24 if not os.path.exists(xenaBaseDir): | |
| 25 os.mkdir(xenaBaseDir) | |
| 26 self.pidfile_path = xenaBaseDir + "/xena-daemon.pid" | |
| 27 | |
| 28 self.stdin_path = '/dev/null' | |
| 29 self.stdout_path = '/dev/null' | |
| 30 self.stderr_path = '/dev/null' | |
| 31 self.pidfile_timeout = 5 | |
| 32 | |
| 33 def run(self): | |
| 34 while True: | |
| 35 #Main code goes here ... | |
| 36 #Note that logger level needs to be set to logging.DEBUG before this shows up in the logs | |
|
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14aaed60e07b
Removed the obsolete --no-auto switch when invoking xena
melissacline
parents:
0
diff
changeset
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37 xenaCmdline = "java -jar %s -r %s/files -d %s/db -t %s/tmp --logfile %s/xena.log -p %s -H 0.0.0.0" |
| 0 | 38 xenaBaseDir = xena.baseDir() |
| 39 xenaCmd = xenaCmdline % (xena.jarPath(), xenaBaseDir, | |
| 40 xenaBaseDir, xenaBaseDir, | |
| 41 xenaBaseDir, xena.port()) | |
| 42 logger.debug("Invoking Xena VM with command %s" % (xenaCmd)) | |
| 43 xenaVm = subprocess.call(xenaCmd, shell=True) | |
| 44 logger.info("Starting Xena VM") | |
| 45 #logger.warn("Warning message") | |
| 46 #logger.error("Error message") | |
| 47 | |
| 48 | |
| 49 | |
| 50 def processListeningOnPort(portID): | |
| 51 cmd = "lsof -t -i :%s -sTCP:LISTEN" % portID | |
| 52 pid = subprocess.check_output(cmd, shell=True).rstrip() | |
| 53 return(int(pid)) | |
| 54 | |
| 55 | |
| 56 fp = open(sys.argv[2], "w") | |
| 57 | |
| 58 app = App() | |
| 59 logger = logging.getLogger("DaemonLog") | |
| 60 logger.setLevel(logging.DEBUG) | |
| 61 formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") | |
| 62 handler = logging.FileHandler(xena.baseDir() + "/xena-daemon.log") | |
| 63 handler.setFormatter(formatter) | |
| 64 logger.addHandler(handler) | |
| 65 | |
| 66 hostname = subprocess.check_output("hostname -f", shell=True).rstrip() | |
| 67 | |
| 68 # | |
| 69 # Check if there has been a Xena running on this system, and | |
| 70 # what its port number is or was. | |
| 71 # | |
| 72 xenaPort = xena.port() | |
| 73 if xenaPort == None: | |
| 74 # In this case, no Xena has been running on this sytem. | |
| 75 xenaIsRunning = False | |
| 76 else: | |
| 77 xenaIsRunning = xena.isRunning(xenaPort) | |
| 78 #rint "xena running", xenaIsRunning, "port", xenaPort | |
| 79 | |
| 80 | |
| 81 if sys.argv[1] == "status": | |
| 82 # | |
| 83 # When checking status, if Xena is running, then report that it's running | |
| 84 # with hostname and port. If it's not running, then report as such. | |
| 85 # | |
| 86 if xenaIsRunning: | |
| 87 fp.write("Xena VM currently running on %s:%s\n" % (hostname, xenaPort)) | |
| 88 fp.write("You can add %s:%s to Xena Data Hub\n" % (hostname, xenaPort)) | |
| 89 else: | |
| 90 fp.write("Xena VM is not currently running on %s\n" % (hostname)) | |
| 91 | |
| 92 elif sys.argv[1] == "start": | |
| 93 # | |
| 94 # When a start command came in, allocate a new port and prepare to start | |
| 95 # xena if it's not already running. If it is already running, then | |
| 96 # report as such. In either case, close the output file before this | |
| 97 # process goes into daemon mode. | |
| 98 # | |
| 99 if not xenaIsRunning: | |
| 100 xenaPort = xena.port(testIfAvailable=True, findNewPort=True) | |
| 101 fp.write("Starting Xena VM on %s:%s\n" % (hostname, xenaPort)) | |
|
31
bb84d3bc5308
make Xena VM already running on ... message more useful for adding the data hub
jingchunzhu <jingchunzhu@gmail.com>
parents:
30
diff
changeset
|
102 fp.write("You can add http://%s:%s to Xena Data Hub\n" % (hostname, xenaPort)) |
| 0 | 103 else: |
| 104 fp.write("Xena VM already running on %s:%s\n" % (hostname, xenaPort)) | |
|
31
bb84d3bc5308
make Xena VM already running on ... message more useful for adding the data hub
jingchunzhu <jingchunzhu@gmail.com>
parents:
30
diff
changeset
|
105 fp.write("You can add http://%s:%s to Xena Data Hub\n" % (hostname, xenaPort)) |
| 0 | 106 fp.close() |
| 107 | |
| 108 elif sys.argv[1] == "stop": | |
| 109 # | |
| 110 # When stopping Xena, if it's currently running, report that Xena | |
| 111 # is being terminated and clean up the port. If it's not running, | |
| 112 # report as such. | |
| 113 # | |
| 114 if xenaIsRunning: | |
| 115 fp.write("Terminating Xena VM on %s:%s\n" % (hostname, xenaPort)) | |
| 116 else: | |
| 117 fp.write("Xena VM is not currently running on %s\n" % (hostname)) | |
| 118 | |
|
30
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
119 elif sys.argv[1] == "version": |
|
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
120 # check the current xena status |
|
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
121 if xenaIsRunning: |
|
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
122 xenaVersionCmd = "java -jar %s --version" % (xena.jarPath()) |
|
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
123 args =shlex.split(xenaVersionCmd) |
|
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
124 output, error = subprocess.Popen(args, stdout = subprocess.PIPE, stderr= subprocess.PIPE).communicate() |
|
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
125 fp.write("The current Xena server version is %s\n" % (output)) |
|
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
126 else: |
|
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
10
diff
changeset
|
127 fp.write("Xena Server is not currently running on %s, please start the server first, then you can check the server version.\n" % (hostname)) |
| 0 | 128 else: |
| 129 fp.write(("Error: Unexpected command %s" % sys.argv[1])) | |
| 130 | |
| 131 | |
| 132 # | |
| 133 # Here is where the starting and stopping of the Xena daemon takes place. | |
| 134 # | |
| 135 if sys.argv[1] == "start" or (sys.argv[1] == "stop" and xenaIsRunning): | |
| 136 daemon_runner = runner.DaemonRunner(app) | |
| 137 # This ensures that the logger file handle does not get closed during daemonization | |
| 138 daemon_runner.daemon_context.files_preserve=[handler.stream] | |
| 139 try: | |
| 140 daemon_runner.do_action() | |
| 141 except LockTimeout: | |
| 142 # Xena is already running. No need to do anything special, but this | |
| 143 # should be separated from the other exceptions. | |
| 144 pass | |
| 145 except: | |
| 146 exc_type, exc_value, exc_traceback = sys.exc_info() | |
| 147 lines = traceback.format_exception(exc_type, exc_value, exc_traceback) | |
| 148 allLines = ''.join('!! ' + line for line in lines) | |
| 149 fp.write("Unsuccessful: error %s\n" % allLines) | |
| 150 if sys.argv[1] == "stop": | |
| 151 # | |
| 152 # If the Xena stop command has been issued, then kill the Xena | |
| 153 # process. | |
| 154 # | |
| 155 xenaPid = processListeningOnPort(xenaPort) | |
| 156 logger.debug("Attempting to kill process with PID %d" % xenaPid) | |
| 157 os.kill(xenaPid, signal.SIGTERM) | |
| 158 if sys.argv[1] != "start": | |
| 159 fp.close() |