def on_message(self, headers, body):
# FIXME, don't hardcode keepalive topic name:
if headers["destination"] == "/topic/keepalive":
logging.debug("got keepalive message")
response = {
"host": socket.gethostname(),
"script": os.path.basename(__file__),
"timestamp": datetime.now().isoformat(),
}
stomp.send(body=json.dumps(response), destination="/topic/keepalive_response")
return ()
debug_msg = {
"script": os.path.basename(__file__),
"host": socket.gethostname(),
"timestamp": datetime.now().isoformat(),
"message": "received message from %s, before thread" % headers["destination"],
}
stomp.send(body=json.dumps(debug_msg), destination="/topic/keepalive_response")
logging.info("Received stomp message: {message}".format(message=body))
received_obj = None
try:
received_obj = json.loads(body)
except ValueError as e:
logging.error("Received invalid JSON: %s." % body)
return
handle_builder_event(received_obj)
logging.info("Destination: %s" % headers.get("destination"))
# Acknowledge that the message has been processed
self.message_received = True
def on_message(self, headers, body):
# FIXME, don't hardcode keepalive topic name:
if headers['destination'] == '/topic/keepalive':
# by default this log message will not
# be visible (logging level is INFO)
# but can be made visible if necessary:
logging.debug('got keepalive message')
response = {
"host": socket.gethostname(),
"script": os.path.basename(__file__)
}
stomp.send(body=json.dumps(response),
destination="/topic/keepalive_response")
return ()
debug_msg = {
"script":
os.path.basename(__file__),
"host":
socket.gethostname(),
"timestamp":
datetime.now().isoformat(),
"message":
"received message from %s before thread" % headers['destination']
}
stomp.send(body=json.dumps(debug_msg),
destination="/topic/keepalive_response")
logging.debug(debug_msg)
logging.info("on_message() Message received")
# Acknowledge that the message has been received
self.message_received = True
t = threading.Thread(target=do_work, args=(body, ))
t.start()
def on_message(self, headers, body):
# FIXME, don't hardcode keepalive topic name:
if headers['destination'] == '/topic/keepalive':
# by default this log message will not
# be visible (logging level is INFO)
# but can be made visible if necessary:
logging.debug('got keepalive message')
response = {
"host": socket.gethostname(),
"script": os.path.basename(__file__)
}
stomp.send(body=json.dumps(response),
destination="/topic/keepalive_response")
return()
debug_msg = {"script": os.path.basename(__file__),
"host": socket.gethostname(), "timestamp":
datetime.now().isoformat(), "message":
"received message from %s before thread" % headers['destination']}
stomp.send(body=json.dumps(debug_msg),
destination="/topic/keepalive_response")
logging.info("on_message() Message received")
# Acknowledge that the message has been received
self.message_received = True
t = threading.Thread(target=do_work, args=(body,))
t.start()
def on_message(self, headers, body):
# FIXME : The maps defined above seem to be an anti-pattern. Also, it's very odd
# IMHO that we're invoking 'global' here. The variable is in scope and
# we're not attempting any read or assignment.
global r_bioc_map
global shell_ext
global packagebuilder_home
logMsg(" [x] Received %r" % (body,))
try:
received_obj = json.loads(body)
except ValueError:
logMsg("Caught Value error, not a valid JSON object?")
sys.stdout.flush()
return ()
if "job_id" in received_obj.keys(): # ignore malformed messages
job_id = received_obj["job_id"]
bioc_version = received_obj["bioc_version"]
r_version = bioc_r_map[bioc_version]
jobs_dir = os.path.join(packagebuilder_home, "jobs")
if not os.path.exists(jobs_dir):
os.mkdir(jobs_dir)
job_dir = os.path.join(jobs_dir, job_id)
if not os.path.exists(job_dir):
os.mkdir(job_dir)
r_libs_dir = os.path.join(job_dir, "R-libs")
if not os.path.exists(r_libs_dir):
os.mkdir(r_libs_dir)
jobfilename = os.path.join(packagebuilder_home, job_dir, "manifest.json")
jobfile = open(jobfilename, "w")
jobfile.write(body)
jobfile.close
logMsg("Wrote job info to %s." % jobfilename)
shell_cmd = os.path.join(packagebuilder_home, "%s%s" % (builder_id, shell_ext))
logMsg("shell_cmd = %s" % shell_cmd)
builder_log = open(os.path.join(job_dir, "builder.log"), "w")
pid = subprocess.Popen(
[shell_cmd, jobfilename, bioc_version], stdout=builder_log, stderr=subprocess.STDOUT
).pid # todo - somehow close builder_log filehandle if possible
msg_obj = {}
msg_obj["builder_id"] = builder_id
msg_obj["body"] = "Got build request..."
msg_obj["first_message"] = True
msg_obj["job_id"] = job_id
msg_obj["client_id"] = received_obj["client_id"]
msg_obj["bioc_version"] = bioc_version
json_str = json.dumps(msg_obj)
stomp.send(destination="/topic/builderevents", body=json_str, headers={"persistent": "true"})
# logMsg("Receipt: %s" % this_frame.headers.get('receipt-id'))
else:
logMsg("Invalid JSON (missing job_id key)")
sys.stdout.flush()
# Acknowledge that the message has been processed
self.message_received = True
def on_message(self, headers, body):
# FIXME, don't hardcode keepalive topic name:
if headers['destination'] == '/topic/keepalive':
logging.debug('got keepalive message')
response = {"host": socket.gethostname(),
"script": os.path.basename(__file__),
"timestamp": datetime.now().isoformat()}
stomp.send(body=json.dumps(response),
destination="/topic/keepalive_response")
return()
debug_msg = {"script": os.path.basename(__file__),
"host": socket.gethostname(), "timestamp":
datetime.now().isoformat(), "message":
"received message from %s" % headers['destination']}
stomp.send(body=json.dumps(debug_msg),
destination="/topic/keepalive_response")
logging.info("Received stomp message with body: {message}".format(message=body))
destination = headers.get('destination')
logging.info("Message is intended for destination: {dst}".format(dst = destination))
received_obj = None
if not is_connection_usable():
logging.info("on_message() Closing connection.")
connection.close()
try:
logging.debug("on_message() Parsing JSON.")
received_obj = json.loads(body)
logging.info("on_message() Successfully parsed JSON")
except ValueError as e:
logging.error("on_message() JSON is invalid: %s." % body)
return
if ('job_id' in received_obj.keys()):
if (destination == '/topic/buildjobs'):
handle_job_start(received_obj)
elif (destination == '/topic/builderevents'):
handle_builder_event(received_obj)
logging.info("on_message() Destination handled.")
else:
logging.warning("on_message() Invalid json (no job_id key).")
# Acknowledge that the message has been processed
self.message_received = True
obj = {}
issue_id = sys.argv[1]
url = sys.argv[2]
segs = url.split("/")
pkgname = segs[4]
pkgname_bare = pkgname.split("_")[0]
obj['force'] = True
obj['bioc_version'] = BIOC_VERSION
obj['r_version'] = BIOC_R_MAP[BIOC_VERSION]
obj['svn_url'] = url
obj['repository'] = 'scratch'
now = pacific.localize(now0)
timestamp1 = now.strftime("%Y%m%d%H%M%S")
timestamp2 = now.strftime("%a %b %d %Y %H:%M:%S")
timestamp2 = timestamp2 + " GMT-%s (%s)" % (offset, tzname)
obj['job_id'] = "%s_%s" % (pkgname_bare, timestamp1)
obj['time'] = timestamp2
obj['client_id'] = "single_package_builder_autobuild:%s:%s" % (issue_id, pkgname)
json = json.dumps(obj)
logging.debug("Received JSON object: '%s'", json)
try:
stomp = getNewStompConnection('', MyListener())
except:
logging.info("Cannot connect")
raise
this_frame = stomp.send(TOPICS['jobs'], json)
TIMEOUT = 60 # timeout in seconds
logging.basicConfig(format='%(levelname)s: %(asctime)s %(message)s',
datefmt='%m/%d/%Y %I:%M:%S %p',
level=logging.INFO)
logging.getLogger("stomp.py").setLevel(logging.WARNING)
class MyListener(ConnectionListener):
def on_message(self, headers, message):
logging.info(message)
try:
logging.info("Attempting to connect using new communication module")
stomp = getNewStompConnection('', MyListener())
# stomp.set_listener('', PrintingListener())
stomp.subscribe(destination="/topic/keepalive_response", id=1, ack='auto')
logging.info("Connection established using new communication module")
except Exception as e:
logging.error("main() Could not connect to ActiveMQ: %s." % e)
raise
while True:
stomp.send(destination="/topic/keepalive", body="stay alive!")
# level is set to info to keep logs quiet, change to info if
# you want to see the following.
logging.debug("Sent keepalive message.")
time.sleep(TIMEOUT)
def do_work(body):
debug_msg = {
"script": os.path.basename(__file__),
"host": socket.gethostname(),
"timestamp": datetime.now().isoformat(),
"message": "received message in thread"
}
stomp.send(body=json.dumps(debug_msg),
destination="/topic/keepalive_response")
logging.info("on_message() Message acknowledged")
try:
received_obj = json.loads(body)
except ValueError:
logging.error("on_message() ValueError: invalid JSON?")
return ()
if ('job_id' in received_obj.keys()): # ignore malformed messages
try:
job_id = received_obj['job_id']
# job_base = job_id.rsplit("_", 1)[0]
job_base = received_obj['client_id'].rsplit(":")[1]
bioc_version = received_obj['bioc_version']
job_dir = os.path.join(ENVIR['spb_home'], "jobs")
if not os.path.exists(job_dir):
os.mkdir(job_dir)
# create package specific directory under jobs/
job_dir_main = os.path.join(job_dir, job_base)
if not os.path.exists(job_dir_main):
os.mkdir(job_dir_main)
# create package specific R-libs directory for package dependencies
r_libs_dir = os.path.join(job_dir_main, "R-libs")
if not os.path.exists(r_libs_dir):
os.mkdir(r_libs_dir)
# create package/github commit specific directory
url_name = received_obj['svn_url'].split("/")
url_user = url_name[3]
url_pkg = url_name[4]
cmd = "/".join([
"https://api.github.com/repos", url_user, url_pkg,
"commits/HEAD"
])
#request = Request(cmd)
try:
#response = urlopen(request)
#res = response.read()
request = requests.get(cmd)
res = request.text
run_dir = json.loads(res)['sha'][0:7]
except URLError, err_url:
logging.info('Cannot access github log: %s', err_url)
logging.debug('URL: %s', cmd)
run_dir = job_id
job_dir = os.path.join(job_dir_main, run_dir)
logging.info("Package Working Directory: %s", job_dir)
if not os.path.exists(job_dir):
os.mkdir(job_dir)
jobfilename = os.path.join(ENVIR['spb_home'], job_dir,
"manifest.json")
jobfile = open(jobfilename, "w")
jobfile.write(body)
jobfile.close()
logging.info("on_message() job_dir: '%s'.", job_dir)
# create other imports
os.environ['SPB_HOME'] = ENVIR['spb_home']
# create BBS-specific imports
os.environ['BBS_HOME'] = ENVIR['bbs_home']
os.environ['BBS_SSH_CMD'] = ENVIR['bbs_ssh_cmd'] + " -qi " + ENVIR[
'bbs_RSA_key'] + " -o StrictHostKeyChecking=no"
os.environ['BBS_R_HOME'] = ENVIR['bbs_R_home']
os.environ['BBS_R_CMD'] = ENVIR['bbs_R_cmd']
os.environ['BBS_BIOC_VERSION'] = ENVIR['bbs_Bioc_version']
os.environ['BBS_RSYNC_CMD'] = ENVIR['bbs_rsync_cmd']
os.environ['BBS_RSYNC_RSH_CMD'] = os.environ.get(
'BBS_RSYNC_CMD') + " -e " + os.environ.get('BBS_SSH_CMD')
os.environ['BBS_MODE'] = ENVIR['bbs_mode']
os.environ['BBS_BIOC_VERSIONED_REPO_PATH'] = os.environ.get(
'BBS_BIOC_VERSION') + "/" + os.environ.get('BBS_MODE')
os.environ['BBS_STAGE2_R_SCRIPT'] = os.environ.get(
'BBS_HOME') + "/" + os.environ.get(
'BBS_BIOC_VERSIONED_REPO_PATH') + "/STAGE2.R"
os.environ['BBS_NON_TARGET_REPOS_FILE'] = os.environ.get(
'BBS_HOME') + "/" + os.environ.get(
'BBS_BIOC_VERSIONED_REPO_PATH') + "/non_target_repos.txt"
os.environ['BBS_CENTRAL_RHOST'] = ENVIR['bbs_central_rhost']
os.environ['BBS_CENTRAL_RUSER'] = ENVIR['bbs_central_ruser']
os.environ['BBS_CENTRAL_RDIR'] = "/home/" + os.environ.get(
'BBS_CENTRAL_RUSER') + "/public_html/BBS/" + os.environ.get(
'BBS_BIOC_VERSIONED_REPO_PATH')
os.environ['BBS_CENTRAL_BASEURL'] = "http://" + os.environ.get(
'BBS_CENTRAL_RHOST') + "/BBS/" + os.environ.get(
'BBS_BIOC_VERSIONED_REPO_PATH')
os.environ['BBS_CURL_CMD'] = ENVIR['bbs_curl_cmd']
os.environ['LANG'] = ENVIR['bbs_lang']
# R CMD check variables
os.environ['R_CHECK_ENVIRON'] = ENVIR['r_check_environ']
os.environ['BIOC_DEVEL_PASSWORD'] = ENVIR['bioc_devel_password']
shell_cmd = [
"python", "-m", "workers.builder", jobfilename, bioc_version
]
builder_log = open(os.path.join(job_dir, "builder.log"), "w")
logging.info(
"on_message() Attempting to run commands from directory: '%s'",
os.getcwd())
logging.info("on_message() shell_cmd: '%s'", shell_cmd)
logging.info("on_message() jobfilename: '%s'", jobfilename)
logging.info("on_message() builder_log: '%s'", builder_log)
blderProcess = subprocess.Popen(shell_cmd,
stdout=builder_log,
stderr=builder_log)
## TODO - somehow close builder_log filehandle if possible
msg_obj = {}
msg_obj['builder_id'] = BUILDER_ID
msg_obj['status'] = "Got Build Request"
msg_obj['body'] = "Got build request..."
msg_obj['first_message'] = True
msg_obj['job_id'] = job_id
msg_obj['client_id'] = received_obj['client_id']
msg_obj['bioc_version'] = bioc_version
json_str = json.dumps(msg_obj)
stomp.send(destination=TOPICS['events'],
body=json_str,
headers={"persistent": "true"})
logging.debug("on_message() Reply sent")
blderProcess.wait()
logging.info(
"on_message() blderProcess finished with status {s}.".format(
s=blderProcess.returncode))
builder_log.close()
logging.info("on_message() builder_log closed.")
except Exception as e:
logging.error("on_message() Caught exception: {e}".format(e=e))
return ()
def do_work(body):
debug_msg = {"script": os.path.basename(__file__),
"host": socket.gethostname(), "timestamp":
datetime.now().isoformat(), "message":
"received message in thread"}
stomp.send(body=json.dumps(debug_msg),
destination="/topic/keepalive_response")
logging.info("on_message() Message acknowledged")
try:
received_obj = json.loads(body)
except ValueError:
logging.error("on_message() ValueError: invalid JSON?")
return()
if ('job_id' in received_obj.keys()): # ignore malformed messages
try:
job_id = received_obj['job_id']
# job_base = job_id.rsplit("_", 1)[0]
job_base = received_obj['client_id'].rsplit(":")[1]
bioc_version = received_obj['bioc_version']
job_dir = os.path.join(ENVIR['spb_home'], "jobs")
if not os.path.exists(job_dir):
os.mkdir(job_dir)
# create package specific directory under jobs/
job_dir_main = os.path.join(job_dir, job_base)
if not os.path.exists(job_dir_main):
os.mkdir(job_dir_main)
# create package specific R-libs directory for package dependencies
r_libs_dir = os.path.join(job_dir_main, "R-libs")
if not os.path.exists(r_libs_dir):
os.mkdir(r_libs_dir)
# create package/github commit specific directory
url_name = received_obj['svn_url'].split("/")
url_user = url_name[3]
url_pkg = url_name[4]
cmd = "/".join(["https://api.github.com/repos",url_user,
url_pkg, "commits/HEAD"])
request = Request(cmd)
try:
response = urlopen(request)
res = response.read()
run_dir = json.loads(res)['sha'][0:7]
except URLError, err_url:
logging.info('Cannot access github log: %s', err_url)
run_dir = job_id
job_dir = os.path.join(job_dir_main, run_dir)
logging.info("Package Working Directory: %s", job_dir)
if not os.path.exists(job_dir):
os.mkdir(job_dir)
jobfilename = os.path.join(ENVIR['spb_home'], job_dir,
"manifest.json")
jobfile = open(jobfilename, "w")
jobfile.write(body)
jobfile.close()
logging.info("on_message() job_dir: '%s'.", job_dir)
# create other imports
os.environ['SPB_HOME'] = ENVIR['spb_home']
# create BBS-specific imports
os.environ['BBS_HOME'] = ENVIR['bbs_home']
os.environ['BBS_SSH_CMD'] = ENVIR['bbs_ssh_cmd'] + " -qi " + ENVIR['bbs_RSA_key'] + " -o StrictHostKeyChecking=no"
os.environ['BBS_R_HOME'] = ENVIR['bbs_R_home']
os.environ['BBS_R_CMD'] = ENVIR['bbs_R_cmd']
os.environ['BBS_BIOC_VERSION'] = ENVIR['bbs_Bioc_version']
os.environ['BBS_RSYNC_CMD'] = ENVIR['bbs_rsync_cmd']
os.environ['BBS_RSYNC_RSH_CMD'] = os.environ.get('BBS_RSYNC_CMD') + " -e " + os.environ.get('BBS_SSH_CMD')
os.environ['BBS_MODE'] = ENVIR['bbs_mode']
os.environ['BBS_BIOC_VERSIONED_REPO_PATH'] = os.environ.get('BBS_BIOC_VERSION') + "/" + os.environ.get('BBS_MODE')
os.environ['BBS_STAGE2_R_SCRIPT'] = os.environ.get('BBS_HOME') + "/" + os.environ.get('BBS_BIOC_VERSIONED_REPO_PATH') + "/STAGE2.R"
os.environ['BBS_NON_TARGET_REPOS_FILE'] = os.environ.get('BBS_HOME') + "/" + os.environ.get('BBS_BIOC_VERSIONED_REPO_PATH') + "/non_target_repos.txt"
os.environ['BBS_CENTRAL_RHOST'] = ENVIR['bbs_central_rhost']
os.environ['BBS_CENTRAL_RUSER'] = ENVIR['bbs_central_ruser']
os.environ['BBS_CENTRAL_RDIR'] = "/home/" + os.environ.get('BBS_CENTRAL_RUSER') + "/public_html/BBS/" + os.environ.get('BBS_BIOC_VERSIONED_REPO_PATH')
os.environ['BBS_CENTRAL_BASEURL'] = "http://" + os.environ.get('BBS_CENTRAL_RHOST') + "/BBS/" + os.environ.get('BBS_BIOC_VERSIONED_REPO_PATH')
os.environ['BBS_CURL_CMD'] = ENVIR['bbs_curl_cmd']
os.environ['LANG'] = ENVIR['bbs_lang']
# R CMD check variables
os.environ['_R_CHECK_TIMINGS_']="0"
os.environ['_R_CHECK_EXECUTABLES_']="FALSE"
os.environ['_R_CHECK_EXECUTABLES_EXCLUSIONS_']="FALSE"
# R CMD BiocCheck variable
os.environ['BIOC_DEVEL_PASSWORD'] = ENVIR['bioc_devel_password']
shell_cmd = ["python", "-m", "workers.builder", jobfilename, bioc_version]
builder_log = open(os.path.join(job_dir, "builder.log"), "w")
logging.info("on_message() Attempting to run commands from directory: '%s'", os.getcwd())
logging.info("on_message() shell_cmd: '%s'", shell_cmd)
logging.info("on_message() jobfilename: '%s'", jobfilename)
logging.info("on_message() builder_log: '%s'", builder_log)
blderProcess = subprocess.Popen(shell_cmd, stdout=builder_log, stderr=builder_log)
## TODO - somehow close builder_log filehandle if possible
msg_obj = {}
msg_obj['builder_id'] = BUILDER_ID
msg_obj['status'] = "Got Build Request"
msg_obj['body'] = "Got build request..."
msg_obj['first_message'] = True
msg_obj['job_id'] = job_id
msg_obj['client_id'] = received_obj['client_id']
msg_obj['bioc_version'] = bioc_version
json_str = json.dumps(msg_obj)
stomp.send(destination=TOPICS['events'], body=json_str,
headers={"persistent": "true"})
logging.info("on_message() Reply sent")
blderProcess.wait()
logging.info("on_message() blderProcess finished with status {s}.".format(s=blderProcess.returncode))
builder_log.close()
logging.info("on_message() builder_log closed.")
except Exception as e:
logging.error("on_message() Caught exception: {e}".format(e=e))
return()
