def main(argv):
expected_major_version = get_options(argv[1:])
print("Expected major version: {}".format(expected_major_version))
installed_version = get_apt_package_version("datadog-agent")
print("Installed Agent version: {}".format(installed_version))
result = check_major_version(installed_version, expected_major_version)
if result:
print("Agent version check successful!")
else:
print("Agent version check failed.")
sys.exit(1)
# expected_major_version
if expected_major_version:
if check_install_info(expected_major_version):
print("install_info check successful!")
else:
print("install_info check failed.")
sys.exit(1)
else:
print("Skipping install_info check.")
sys.exit()
def process_request(self,req):
options = get_options(self.config)
build_type_match = re.match('/builds/history/(bt\d+)?$',req.path_info)
if build_type_match is None:
query_string = "&".join(['buildTypeId=%s' % id for id in options['builds']])
else:
build_type_id = build_type_match.groups()[0]
query_string = 'buildTypeId=%s' % build_type_id
add_stylesheet(req, 'teamcity/css/teamcity.css')
query_string += '&sinceDate=-%d' % options['limit']
feed_url = "%s/feed.html?%s" % (options['base_url'], query_string)
tc = TeamCityQuery(self.options)
feed = TeamCityQuery.xml_query(feed_url)
if feed is None:
raise HTTPNotFound("Can't load feed")
data = {'entries': []}
for entry in feed.iterfind('{http://www.w3.org/2005/Atom}entry'):
title = entry.find('{http://www.w3.org/2005/Atom}title').text
link = entry.find('{http://www.w3.org/2005/Atom}link').attrib['href']
date = entry.find('{http://www.w3.org/2005/Atom}published').text
date = datetime.strptime(date, '%Y-%m-%dT%H:%M:%SZ')
summary = entry.find('{http://www.w3.org/2005/Atom}summary').text
summary = summary.split('<a href')[0]
build_id_match = re.search('buildId=(\d+)', link)
if build_id_match:
summary += "<br/><a href='%s'>Build Log</a>" % \
req.href.builds('download', build_id_match.groups()[0])
data['entries'].append({
'title': title,
'link': link,
'date': date,
'summary': summary,
})
return 'teamcity_status.html', data, None
def main():
points = get_points()
options = get_options()
options['outdir'] = '/tmp/'
options['prefix'] = 'concave'
concave, convex = get_concave(points)
draw(options, concave, points, convex)
def main():
points = get_points()
options = get_options()
options['outdir'] = '/tmp/'
options['prefix'] = 'concave'
concave, convex = get_concave(points)
draw(options, concave, points, convex)
def __init__(self):
self.options = get_options(self.config)
self.msg_cache_dir = self.options['cache_dir'] or '/tmp/teamcity_cache'
if not os.path.exists(self.msg_cache_dir):
try:
os.mkdir(self.msg_cache_dir)
except OSError,e:
self.log.error("Can't create cache_dir: %s" % e)
def main():
parser = argparse.ArgumentParser(
description='Plot data stored in an sqlite database')
parser.add_argument('--outdir',
default='./',
help='output directory for the plots')
parser.add_argument('--fontsize',
default=matplotlib.rcParams['font.size'],
type=int,
help='base font size of plots')
parser.add_argument('--nodes',
'-N',
default=50,
type=int,
help='nodes thay apply restart')
parser.add_argument('--qd',
default=0.7,
type=float,
help='loss independent of tau')
parser.add_argument('--ES',
default=0.05,
type=float,
help='expexted network sojourn time')
parser.add_argument('--deadline',
'-T',
default=15,
type=float,
help='deadline')
parser.add_argument('--threshold',
'-m',
default=5,
type=int,
help='threshold for jobs in the queue')
parser.add_argument('--max_tau',
default=10,
type=float,
help='maximum tau (bounded by T)')
args = parser.parse_args()
options = get_options()
options['prefix'] = 'restart'
options['outdir'] = args.outdir
options['fontsize'] = args.fontsize
options['nodes'] = args.nodes
options['qd'] = args.qd
options['ES'] = args.ES
options['deadline'] = args.deadline
options['threshold'] = args.threshold
options['max_tau'] = min(args.max_tau, args.deadline)
plot(options)
def main(argv):
expected_major_version = get_options(argv[1:])
print("Expected major version: {}".format(expected_major_version))
installed_version = get_yum_package_version("datadog-agent")
print("Installed Agent version: {}".format(installed_version))
result = check_major_version(installed_version, expected_major_version)
if result:
print("Agent version check successful!")
sys.exit()
else:
print("Agent version check failed.")
sys.exit(1)
def render_admin_panel(self, req, category, page, path_info):
if not req.perm.has_permission('TEAMCITY_ADMIN'):
raise HTTPForbidden('You are not allowed to configure TC plugin')
if req.method == 'POST':
options, errors = self._save_options(req.args)
if not errors:
# redirect here
req.redirect(req.href(req.path_info))
else:
options, errors = get_options(self.config), []
tc = TeamCityQuery(options)
url = "%s/httpAuth/app/rest/buildTypes" % options['base_url']
# load builds from TC using REST API
try:
builds_xml = tc.xml_query(url)
except TeamCityError, e:
errors.append("Fix base config options: %s" % e)
t_data = {'options': options, 'projects': {}, 'errors': errors}
return 'teamcity_admin.html', t_data
def render_admin_panel(self,req,category,page,path_info):
if not req.perm.has_permission('TEAMCITY_ADMIN'):
raise HTTPForbidden('You are not allowed to configure TC plugin')
if req.method == 'POST':
options,errors = self._save_options(req.args)
if not errors:
# redirect here
req.redirect(req.href(req.path_info))
else:
options,errors = get_options(self.config),[]
tc = TeamCityQuery(options)
url = "%s/httpAuth/app/rest/buildTypes" % options['base_url']
# load builds from TC using REST API
try:
builds_xml = tc.xml_query(url)
except TeamCityError,e:
errors.append("Fix base config options: %s" % e)
t_data = {'options':options,'projects':{},'errors':errors}
return 'teamcity_admin.html',t_data
#!/usr/bin/python
from ruffus import *
import yaml
import os
import tasks
import helpers
# Config ---------------------------------------------------------------------
# Set up command line option handling, logger creation, and load config file
options = helpers.get_options()
logger_proxy, logging_mutex = helpers.make_logger(options, __file__)
config = yaml.load(open(options.config).read())
def report(result):
"""Wrapper around Result.report"""
result.report(logger_proxy, logging_mutex)
# Pipeline -------------------------------------------------------------------
@files(list(tasks.fastq_to_other_files(config, extension='.clipped')))
def clip(infile, outfile):
result = tasks.clip(infile, outfile, config)
@transform(clip, suffix('.clipped'), '.clipped.bowtie.sam')
def map(infile, outfile):
result = tasks.bowtie(infile, outfile, config)
report(result)
from os.path import (
join, expanduser, expandvars,
splitext,split, basename, dirname, exists
)
helpers.setup_shell_environment()
import tasks
import glob
#import pyprind
from termcolor import colored
import datetime
is_64bits = sys.maxsize > 2**32
#import graphviz
if not is_64bits:
print "Please upgrade your operating system to 64 bit, application such as diamond don't run on 32 bit"
sys.exit(0)
options = helpers.get_options()
#logger_proxy, logging_mutex = helpers.make_logger(options, __file__)
basedir = os.path.relpath('./')
projectDir = options.outdir # set output dir
proDir= os.path.basename(projectDir)
print proDir
inputDir = options.fastq_file
inputDir = os.path.abspath(inputDir)# get fastq.gz file
print inputDir
dir_name = basename(inputDir)
probe = os.path.abspath(options.probe_file)
probPath, probFile = os.path.split(probe)
print probe
#plateWall_bc = os.path.abspath(options.sample_sheet)
def __init__(self):
self.options = get_options(self.config)
def __init__(self): self.options = get_options(self.config)
def process_request(self,req):
if not req.perm.has_permission('TEAMCITY_BUILD'):
raise HTTPForbidden('You are not allowed to view/run TC builds')
options = get_options(self.config)
tc = TeamCityQuery(options)
# projects variable will collect builds result in following format:
# {'projectId': {
# 'name': 'Proj1',
# 'btypes': [{ # it's a list of build types assigned to this project
# 'btype_id': 'bt1',
# 'btype_name': 'PS3 builds'
# 'build': {
# 'number': 5555 # teamcity number
# 'status': 'Success',
# 'start_date': datetime_object,
# 'end_date': datetime_object,
# },]
# }
# }
projects = {}
for build_type in options['builds']:
# load builds xml from teamcity
url = "%s/httpAuth/app/rest/buildTypes/id:%s/builds" %\
(options['base_url'],build_type)
btype_xml = tc.xml_query(url)
if btype_xml is None:
self.log.error("Can't load builds xml at %s" % url)
continue
if len(btype_xml) < 1: # there is not any builds yet
url = '%s/httpAuth/app/rest/buildTypes/id:%s' % (options['base_url'], build_type)
build_xml = tc.xml_query(url)
if build_xml is None:
continue
proj_id = build_xml.xpath('/buildType/project/@id')[0]
# collect here as many build info as possible and continue
build_info = {
'btype_id': build_type,
'btype_name': build_xml.attrib['name'],
'build': {
'id': None,
'number': None,
'status': 'unknown',
'end_date': 'Never',
'duration': 'Unknown'
}
}
if proj_id in projects:
projects[proj_id]['btypes'].append(build_info)
else: # or create new item in projects
projects[proj_id] = {
'name': proj_name,
'btypes': [build_info,]
}
continue
# There is at least one finished build
last_build = btype_xml[0].attrib
# load this build xml
url = "%s%s" % (options['base_url'],last_build['href'])
build_xml = tc.xml_query(url)
if build_xml is None:
self.log.error("Can't load build xml at %s" % url)
proj_id = build_xml.xpath('/build/buildType/@projectId')[0]
proj_name = build_xml.xpath('/build/buildType/@projectName')[0]
# F**k! python2.5 has not support for timezones in datetime.strptime
try:
# datetime lacks timezone info
start_date = build_xml.xpath('/build/startDate/text()')[0].split('+')[0]
start_date = datetime.strptime(start_date, '%Y%m%dT%H%M%S')
# datetime lacks timezone info
end_date = build_xml.xpath('/build/finishDate/text()')[0].split('+')[0]
end_date = datetime.strptime(end_date, '%Y%m%dT%H%M%S')
except IndexError: # no start_date or end_date, duration is unknown
end_date = 'Never'
duration = 'Unknown'
else:
duration = end_date - start_date
# parse build status
try:
status = build_xml.xpath('/build/statusText/text()')[0].lower()
except IndexError: # no last status yet
status = 'unknown'
# result build dictionary
build_info = {
'btype_id': build_type,
'btype_name': build_xml.xpath('/build/buildType/@name')[0],
'build': {
'id': build_xml.attrib['id'],
'number': build_xml.attrib['number'],
'status': status,
'end_date': end_date,
'duration': duration
}
}
# add new build to project
if proj_id in projects:
projects[proj_id]['btypes'].append(build_info)
else: # or create new item in projects
projects[proj_id] = {
'name': proj_name,
'btypes': [build_info,]
}
add_stylesheet(req,'teamcity/css/teamcity.css')
add_javascript(req,'teamcity/js/jquery.timers-1.2.js')
add_javascript(req,'teamcity/js/event_tracker.js')
return 'teamcity_builds.html', {
'projects':projects,
'dpath':req.href('builds/download')
}, None
def main():
"""
The main function of the plotting module
"""
parser = argparse.ArgumentParser(description='Plot data stored in an sqlite database')
parser.add_argument('--db', default='./sqlite.db', help='name of the database where the parsed and evaluated data is stored')
parser.add_argument('--src', nargs='+', default=['all'], help='source node sending packets')
parser.add_argument('--bins', default=10, type=int, help='granularity of the 3d box plot; bin size')
parser.add_argument('--fix', nargs='+', default=[0], type=int, help='fix the number of parallel sources when routers failed [steps]')
parser.add_argument('--outdir', default='', help='output directory for the plots')
parser.add_argument('--fontsize', default=matplotlib.rcParams['font.size'], type=int, help='base font size of plots')
parser.add_argument('--username', help='username for the database access to get the nodes\' positions')
parser.add_argument('--password', help='password for the database access to get the nodes\' positions')
parser.add_argument('--dbhost', default='uhu.imp.fu-berlin.de', help='hostname for the database access to get the nodes\' positions')
parser.add_argument('--execute', '-e', nargs='+', default=['all'], help='Execute the specified functions')
parser.add_argument('--list', nargs='?', const=True, default=False, help='List all callable plotting functions')
parser.add_argument('--update', nargs='?', const=True, default=False, help='Download or update data from the testbed database')
parser.add_argument('--statistics', nargs='?', const=True, default=False, help='Calculate and plot distance statistics')
parser.add_argument('--deadline', default=40, type=float, help='Maximum time for the retransmit plot')
parser.add_argument('--restarts', default=numpy.infty, type=float, help='Maximum number of retransmsmissions to plot')
parser.add_argument('--repetitions', default=13, type=int, help='for MPR phi plotting')
parser.add_argument('--intervals', nargs='+', default=[], type=float, help='Selected intervals for the evaluation')
parser.add_argument('--special', nargs='+', default=[''], help='Special options for the plots')
parser.add_argument('--mark', nargs='+', default=[], type=int, help='Mark p_s in plots for sources')
parser.add_argument('--grayscale', nargs='?', const=True, default=False, help='Create plots with grayscale colormap')
args = parser.parse_args()
if args.list:
print('Callable plot functions:')
for func in sorted([key for key in globals().keys() if key.startswith('plot_')]):
print('\t'+func)
sys.exit(0)
logging.basicConfig(level=logging.INFO, format='%(levelname)s [%(funcName)s] %(message)s')
options = get_options()
options['db'] = args.db
options['src'] = args.src
options['bins'] = args.bins
options['outdir'] = args.outdir
options['fontsize'] = args.fontsize
options['username'] = args.username
options['dbpassword'] = args.password
options['fix'] = args.fix
options['dbhost'] = args.dbhost
options['show3d'] = False
options['statistics'] = args.statistics
options['restarts'] = args.restarts
options['deadline'] = args.deadline
options['intervals'] = args.intervals
options['special'] = args.special
options['mark'] = args.mark
options['repetitions'] = args.repetitions
options['grayscale'] = args.grayscale
db = options["db"]
conn = sqlite3.connect(db)
options['db_conn'] = conn
cursor = conn.cursor()
options['neg_rssi'] = False
logging.info('old or new rssi format?')
#max_rssi = max(cursor.execute('''SELECT rssi FROM rx WHERE NOT rssi=0 LIMIT 1''').fetchone()[0], cursor.execute('''SELECT rssi FROM rx WHERE NOT rssi=0 LIMIT 1''').fetchone()[0])
#if max_rssi>0:
#options['neg_rssi'] = False
logging.basicConfig(level=logging.INFO, format='%(levelname)s [%(funcName)s] %(message)s')
logging.info('connecting to database')
if args.update:
logging.info('updating positions from %s', options['dbhost'])
update_data(options)
sys.exit(0)
if 'all' in args.src:
logging.info('all sources selected for plotting')
try:
cursor.execute('''
CREATE TABLE eval_sources (
host TEXT NOT NULL,
FOREIGN KEY(host) REFERENCES addr(host)
)
''')
logging.info('extracting all source node names')
cursor.execute('''
INSERT INTO eval_sources
SELECT DISTINCT(host)
FROM tx
ORDER BY host
''')
conn.commit()
except sqlite3.OperationalError:
pass
sources = cursor.execute('''
SELECT DISTINCT(host)
FROM eval_sources
ORDER BY host
''').fetchall()
options['src'] = list(pylab.flatten(sources))
prepare_outdir(options)
open_latex_file(options)
eval_scenarios(options)
write_scenarios(options)
#try:
prepare_coordinates(options)
#except ValueError:
#logging.warning('no router positions found in DB')
if 'all' in args.execute:
for func in [globals()[key] for key in globals().keys() if key.startswith('plot_')]:
func(options)
else:
for func in args.execute:
try:
globals()[func](options)
except KeyError:
logging.critical('function not found: %s' % func)
raise
cursor.close()