Mercurial > repos > melissacline > ucsc_xena_platform
annotate runXena.py @ 46:cdba6c63dce5
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| author | jingchunzhu |
|---|---|
| date | Wed, 29 Jul 2015 10:26:18 -0700 |
| parents | a3fbe077a14c |
| children |
| 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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9 import subprocess, shlex |
| 0 | 10 import sys |
| 11 import time | |
| 12 import traceback | |
| 13 import xena_utils as xena | |
| 14 | |
| 33 | 15 dirname = os.path.dirname(os.path.abspath(sys.argv[0])) |
| 16 | |
| 17 sys.path.insert(0, dirname + "/lockfile-0.10.2/") | |
| 18 sys.path.insert(0, dirname + "/python-daemon-2.0.5/") | |
| 19 | |
| 20 | |
| 0 | 21 #third party libs |
| 22 from daemon import runner | |
| 23 from lockfile import LockTimeout | |
| 24 | |
| 25 | |
| 26 class App(): | |
| 27 | |
| 28 def __init__(self): | |
| 29 xenaBaseDir = xena.baseDir() | |
| 30 if not os.path.exists(xenaBaseDir): | |
| 31 os.mkdir(xenaBaseDir) | |
| 32 self.pidfile_path = xenaBaseDir + "/xena-daemon.pid" | |
| 33 | |
| 34 self.stdin_path = '/dev/null' | |
| 35 self.stdout_path = '/dev/null' | |
| 36 self.stderr_path = '/dev/null' | |
| 37 self.pidfile_timeout = 5 | |
| 38 | |
| 39 def run(self): | |
| 40 while True: | |
| 41 #Main code goes here ... | |
| 42 #Note that logger level needs to be set to logging.DEBUG before this shows up in the logs | |
| 33 | 43 xenaCmdline = "java -jar %s -r %s/files -d %s/db -t %s/tmp --no-gui --logfile %s/xena.log -p %s -H 0.0.0.0" |
| 0 | 44 xenaBaseDir = xena.baseDir() |
| 45 xenaCmd = xenaCmdline % (xena.jarPath(), xenaBaseDir, | |
| 46 xenaBaseDir, xenaBaseDir, | |
| 47 xenaBaseDir, xena.port()) | |
| 48 logger.debug("Invoking Xena VM with command %s" % (xenaCmd)) | |
| 49 xenaVm = subprocess.call(xenaCmd, shell=True) | |
| 50 logger.info("Starting Xena VM") | |
| 51 #logger.warn("Warning message") | |
| 52 #logger.error("Error message") | |
| 53 | |
| 54 | |
| 55 | |
| 56 def processListeningOnPort(portID): | |
| 57 cmd = "lsof -t -i :%s -sTCP:LISTEN" % portID | |
| 58 pid = subprocess.check_output(cmd, shell=True).rstrip() | |
| 59 return(int(pid)) | |
| 60 | |
| 61 | |
| 62 fp = open(sys.argv[2], "w") | |
| 63 | |
| 64 app = App() | |
| 65 logger = logging.getLogger("DaemonLog") | |
| 66 logger.setLevel(logging.DEBUG) | |
| 67 formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") | |
| 68 handler = logging.FileHandler(xena.baseDir() + "/xena-daemon.log") | |
| 69 handler.setFormatter(formatter) | |
| 70 logger.addHandler(handler) | |
| 71 | |
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parents:
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changeset
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72 hostname = xena.hostname() #subprocess.check_output("hostname -f", shell=True).rstrip() |
| 0 | 73 |
| 74 # | |
| 75 # Check if there has been a Xena running on this system, and | |
| 76 # what its port number is or was. | |
| 77 # | |
| 78 xenaPort = xena.port() | |
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parents:
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79 |
| 0 | 80 if xenaPort == None: |
| 81 # In this case, no Xena has been running on this sytem. | |
| 82 xenaIsRunning = False | |
| 83 else: | |
| 84 xenaIsRunning = xena.isRunning(xenaPort) | |
| 85 #rint "xena running", xenaIsRunning, "port", xenaPort | |
| 86 | |
| 87 | |
| 88 if sys.argv[1] == "status": | |
| 89 # | |
| 90 # When checking status, if Xena is running, then report that it's running | |
| 91 # with hostname and port. If it's not running, then report as such. | |
| 92 # | |
| 93 if xenaIsRunning: | |
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94 fp.write("Xena VM currently running on http://%s:%s\n" % (hostname, xenaPort)) |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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changeset
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95 fp.write("\n") |
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63b1ba1e3424
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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diff
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96 fp.write("You can add http://%s:%s to Xena Data Hub\n" % (hostname, xenaPort)) |
| 0 | 97 else: |
| 98 fp.write("Xena VM is not currently running on %s\n" % (hostname)) | |
| 99 | |
| 100 elif sys.argv[1] == "start": | |
| 101 # | |
| 102 # When a start command came in, allocate a new port and prepare to start | |
| 103 # xena if it's not already running. If it is already running, then | |
| 104 # report as such. In either case, close the output file before this | |
| 105 # process goes into daemon mode. | |
| 106 # | |
| 107 if not xenaIsRunning: | |
| 108 xenaPort = xena.port(testIfAvailable=True, findNewPort=True) | |
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63b1ba1e3424
server status message more accurate -- http
jingchunzhu <jingchunzhu@gmail.com>
parents:
31
diff
changeset
|
109 fp.write("Starting Xena VM on http://%s:%s\n" % (hostname, xenaPort)) |
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a3fbe077a14c
replace wget with python method
jingchunzhu <jingchunzhu@gmail.com>
parents:
33
diff
changeset
|
110 fp.write("\n") |
|
a3fbe077a14c
replace wget with python method
jingchunzhu <jingchunzhu@gmail.com>
parents:
33
diff
changeset
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111 fp.write("Use Xena Administration -> Check Status tool to review status.\n") |
| 0 | 112 else: |
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63b1ba1e3424
server status message more accurate -- http
jingchunzhu <jingchunzhu@gmail.com>
parents:
31
diff
changeset
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113 fp.write("Xena VM already running on http://%s:%s\n" % (hostname, xenaPort)) |
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34
a3fbe077a14c
replace wget with python method
jingchunzhu <jingchunzhu@gmail.com>
parents:
33
diff
changeset
|
114 fp.write("\n") |
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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diff
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115 fp.write("You can add http://%s:%s to Xena Data Hub\n" % (hostname, xenaPort)) |
| 0 | 116 fp.close() |
| 117 | |
| 118 elif sys.argv[1] == "stop": | |
| 119 # | |
| 120 # When stopping Xena, if it's currently running, report that Xena | |
| 121 # is being terminated and clean up the port. If it's not running, | |
| 122 # report as such. | |
| 123 # | |
| 124 if xenaIsRunning: | |
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63b1ba1e3424
server status message more accurate -- http
jingchunzhu <jingchunzhu@gmail.com>
parents:
31
diff
changeset
|
125 fp.write("Terminating Xena VM on http://%s:%s\n" % (hostname, xenaPort)) |
| 0 | 126 else: |
| 127 fp.write("Xena VM is not currently running on %s\n" % (hostname)) | |
| 128 | |
|
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
|
129 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
|
130 # 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
|
131 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
|
132 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
|
133 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
|
134 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
|
135 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
|
136 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
|
137 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 | 138 else: |
| 139 fp.write(("Error: Unexpected command %s" % sys.argv[1])) | |
| 140 | |
| 141 | |
| 142 # | |
| 143 # Here is where the starting and stopping of the Xena daemon takes place. | |
| 144 # | |
| 145 if sys.argv[1] == "start" or (sys.argv[1] == "stop" and xenaIsRunning): | |
| 146 daemon_runner = runner.DaemonRunner(app) | |
| 147 # This ensures that the logger file handle does not get closed during daemonization | |
| 148 daemon_runner.daemon_context.files_preserve=[handler.stream] | |
| 149 try: | |
| 150 daemon_runner.do_action() | |
| 151 except LockTimeout: | |
| 152 # Xena is already running. No need to do anything special, but this | |
| 153 # should be separated from the other exceptions. | |
| 154 pass | |
| 155 except: | |
| 156 exc_type, exc_value, exc_traceback = sys.exc_info() | |
| 157 lines = traceback.format_exception(exc_type, exc_value, exc_traceback) | |
| 158 allLines = ''.join('!! ' + line for line in lines) | |
| 159 fp.write("Unsuccessful: error %s\n" % allLines) | |
| 160 if sys.argv[1] == "stop": | |
| 161 # | |
| 162 # If the Xena stop command has been issued, then kill the Xena | |
| 163 # process. | |
| 164 # | |
| 165 xenaPid = processListeningOnPort(xenaPort) | |
| 166 logger.debug("Attempting to kill process with PID %d" % xenaPid) | |
| 167 os.kill(xenaPid, signal.SIGTERM) | |
| 168 if sys.argv[1] != "start": | |
| 169 fp.close() |