def parseUserProperties(self, plen, prop_delta=False):
start = self.reader.start
properties = UserProperties()
while not self.matchUserPropertyEnd():
assert not self.reader.eof, msg("""
Expected to find a user property, instead found end of file.
""")
if self.matchUserPropertyKey():
key = self.parseUserPropertyKey()
value = self.parseUserPropertyValue()
properties[key] = value
elif self.matchUserPropertyDelete():
assert prop_delta, msg("""
Property deletion (operation 'D') is only allowed
when the Prop-delta dump property is true for the
containing node or revision.
""")
key = self.parseUserPropertyDelete()
properties[key] = None
else:
self.parseUserPropertyEnd()
stop = self.reader.start
assert plen == stop - start, msg(
"""Property-Legnth is incorrect.
Expected %d bytes, but found %d bytes.""" % (
plen, stop - start))
return properties
def main(argv):
# Initialize new external memory list.
util.msg('Populating normal and external memory list')
t1 = time.time()
dirname = util.make_temp_name('em_list')
l = []
em_list = pyrsistence.EMList(dirname)
for i in util.xrange(0x1000000):
v = random.randrange(0x1000000)
em_list.append(v)
l.append(v)
t2 = time.time()
util.msg('Done in %d sec.' % (t2 - t1))
util.msg('Verifying external memory list contents')
for i in util.xrange(0x1000000):
if em_list[i] != l[i]:
util.msg('FATAL! Mismatch in element %d: Got %#x but expected %#x' % (i, em_list[i], l[i]))
t3 = time.time()
util.msg('Done in %d sec.' % (t3 - t2))
# Close and remove external memory list from disk.
em_list.close()
shutil.rmtree(dirname)
return 0
def main(argv):
# Initialize new external memory dictionary.
util.msg('Populating normal and external memory dictionary')
t1 = time.time()
dirname = util.make_temp_name('em_dict')
d = {}
em_dict = pyrsistence.EMDict(dirname)
for i in util.xrange(0x1000000):
v = random.randrange(0x1000000)
em_dict[i] = v
d[i] = v
t2 = time.time()
util.msg('Done in %d sec.' % (t2 - t1))
util.msg('Verifying external memory dictionary contents')
for i in util.xrange(0x1000000):
if em_dict[i] != d[i]:
util.msg('FATAL! Mismatch in element %d: Got %#x but expected %#x' % (i, em_dict[i], d[i]))
t3 = time.time()
util.msg('Done in %d sec.' % (t3 - t2))
# Close and remove external memory dictionary from disk.
em_dict.close()
shutil.rmtree(dirname)
return 0
def addEpisode(xbmcid, scraperid, snr,enr, title, airdate):
f = getDatabase("r")
soup = BeautifulSoup(f.read())
f.close()
serie = soup.find(scraperid = scraperid)
#TODO check inconsistency
if serie == None :
return False
season = serie.find(seasonnr = snr)
if season == None:
tag = Tag(soup, "season")
tag.attrs.append(('seasonnr', snr))
serie.append(tag)
season = serie.find(seasonnr = snr)
if season == None:
util.msg(localize(50000), localize(50004))
return False
episode = season.find(episodenr = enr)
if episode == None:
episodetag = Tag(soup, "episode")
episodetag.attrs.append(('episodenr', enr))
titletag = Tag(soup, "title")
titletag.insert(0,title)
episodetag.append(titletag)
airdatetag = Tag(soup, "airdate")
airdatetag.insert(0,airdate)
episodetag.append(airdatetag)
season.append(episodetag)
f = getDatabase("w")
f.write(soup.prettify())
f.close()
#else:
#check consistency
return True
def __init__(self, fn):
# super constructor
util.FileCache.__init__(self, fn)
# open and map file
f = open(fn)
buf = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
at = 0
# traverse the file reading type 1 chunks
self.chunks = []
metadata = None
while at < len(buf):
try:
chunk_doc = read_bson_doc(buf, at)
at += chunk_doc.bson_len
if chunk_doc['type']==0:
metadata = chunk_doc
elif chunk_doc['type']==1:
self.chunks.append(Chunk(chunk_doc, metadata))
except Exception as e:
util.msg('stopping at bad bson doc (%s)' % e)
return
# bson docs should exactly cover file
assert(at==len(buf))
def dbg(fn, opt, show=True):
def pt(t):
return time.strftime('%Y-%m-%dT%H:%M:%S', time.gmtime(t/1000)) + ('.%03d' % (t%1000))
for metrics in read(None, fn, opt):
if show:
if 'serverStatus.localTime' in metrics:
sslt = metrics['serverStatus.localTime']
util.msg(metrics._id, pt(metrics._id), pt(sslt[0]), pt(sslt[-1]),
'ds', len(sslt), 'ms', len(metrics))
else:
#print 'no serverStatus.localTime'
util.msg(metrics.keys())
def initDatabase():
addon_work_folder = os.path.join(xbmc.translatePath( "special://profile/addon_data/" ), "plugin.program.download-next-ep")
soup = BeautifulSoup("<database><serverTime></serverTime><series></series></database>")
try:
if not os.path.exists(addon_work_folder):
os.makedirs(addon_work_folder)
f = getDatabase("w")
f.write(soup.prettify())
f.close()
#util.msg("file write success","wote file to:\n" +addon_work_folder )
except:
util.msg(localize(50000), localize(50003))
def get_first(self):
# did we already read ref doc and metadata?
if self.state >= 1:
assert(self.metrics)
return self.metrics
# map from metric names to list of values for each metric
# metric names are paths through the sample document
self.metrics = collections.OrderedDict()
self.metrics.metadata = self.metadata
self.metrics._id = self.chunk_doc['_id']
# decompress chunk data field
data = self.chunk_doc['data']
data = data[4:] # skip uncompressed length, we don't need it
data = zlib.decompress(data)
# read reference doc from chunk data, ignoring non-metric fields
ref_doc = read_bson_doc(data, 0, ftdc=True)
#print_bson_doc(ref_doc)
# traverse the reference document and extract metric names
def extract_names(doc, n=''):
for k, v in doc.items():
nn = n + util.SEP + k if n else k
if type(v)==util.BSON:
extract_names(v, nn)
else:
self.metrics[nn] = [v]
extract_names(ref_doc)
# get nmetrics, ndeltas
self.nmetrics = uint32.unpack_from(data, ref_doc.bson_len)[0]
self.ndeltas = uint32.unpack_from(data, ref_doc.bson_len+4)[0]
self.nsamples = self.ndeltas + 1
at = ref_doc.bson_len + 8
if self.nmetrics != len(self.metrics):
# xxx remove when SERVER-20602 is fixed
util.msg('ignoring bad chunk: nmetrics=%d, len(metrics)=%d' % (
self.nmetrics, len(self.metrics)))
return None
#assert(self.nmetrics==len(metrics))
# record data and position in data for decompressing deltas when we need them
self.data = data[at:]
# release the chunk_doc as the needed info is now parsed into self.metrics, self.data, etc.
self.chunk_doc = None
# our result, containing only the first (reference) sample
self.state = 1
return self.metrics
def about(self):
"""prints about message in popup"""
util.msg('''
clark Sonic Commissioning Software
Clark Solutions
Hudson, MA 01749
www.clarksol.com
Version: {0}
By: {1}'''.format(__version__,__author__),'About')
return
def main(argv):
# Initialize new external memory list.
util.msg('Populating external memory list')
t1 = time.time()
dirname = util.make_temp_name('em_list')
em_list = pyrsistence.EMList(dirname)
for i in util.xrange(0x1000):
em_list.append(random.randrange(0x100000))
t2 = time.time()
util.msg('Done in %d sec.' % (t2 - t1))
# Request several iterator objects to locate possible memory leaks.
util.msg('Testing iterator')
for i in util.xrange(0x1000):
for item in em_list:
pass
t3 = time.time()
util.msg('Done in %d sec.' % (t3 - t2))
# Close and remove external memory list from disk.
em_list.close()
shutil.rmtree(dirname)
return 0
def main(opt):
do_server = opt.server
do_html = opt.html
do_connect = opt.connect
do_browser = not opt.server and not opt.html and not opt.connect
if do_browser:
if opt.browser:
util.msg('--browser flag is obsolete; browser mode is now the default')
else:
util.msg('browser mode is now the default; use --html out.html to generate static html')
if do_browser:
do_server = True
# --server or browser mode
if do_server:
httpd = None
for opt.port in range(opt.port, opt.port+100):
try:
Handler.exit_on_close = not opt.server
httpd = BaseHTTPServer.HTTPServer(('', opt.port), Handler)
break
except Exception as e:
util.msg('can\'t open port %d: %s' % (opt.port, e))
if not httpd:
raise e
httpd.ses = Ses(opt, path='/0', server=True) # default session
url = 'http://localhost:%d' % opt.port
util.msg('listening for a browser request for %s' % url)
if do_browser:
browser(opt, url)
httpd.serve_forever()
# --connect
elif do_connect:
args = ' '.join(pipes.quote(s) for s in sys.argv[1:])
args = urllib.urlencode({'args': args})
url = opt.connect + '/open?' + args
browser(opt, url)
# standalone static html
elif do_html:
util.msg('generating html file', do_html)
ses = Ses(opt, server=False)
ses.out = open(do_html, 'w')
html.page(ses)
def parseDumpProperty(self, name=None, store=None):
"""
A dump property consists of a name and a value on a single
line, separated by a colon.
name
If specified: (1) the parsed property must have this
name. (2) we return the value of the property as a string.
If None, then we return a tuple (*name*, *value*), both
strings.
store
If specified, it must be a dictionary. We'll update it as
store[name] = value before we return.
returns
*value* or ( *name*, *value* )
"""
m = pat_dump_property.match(self.reader.cur)
assert m, "Expecting a dump property, but found \n%s" % (self.reader,)
assert name == None or name == m.group(1), msg("""
Expected property %s, but found %s
""" % (name, m.group(1)))
value = m.group(2)
if store != None:
store[m.group(1)] = value
self.reader.next()
if name == None:
return m.group(1), value
else:
return value
def do_POST(self):
util.msg('POST', self.path)
if self.path.endswith('/model'):
path = self.path[:-len('/model')] # strip off /model to get session path
ses = Ses.sessions[path]
l = int(self.headers.getheader('content-length', 0))
data = self.rfile.read(l)
js = json.loads(data)
for name in js:
setattr(ses.opt, name, js[name])
elif self.path=='/save':
l = int(self.headers.getheader('content-length', 0))
req = urlparse.parse_qs(self.rfile.read(l))
fn = req['fn'][0]
open(fn, 'w').write(ses.get_save())
util.msg('saved to', fn)
def main(argv):
# Initialize new external memory list.
util.msg('Populating external memory list')
t1 = time.time()
dirname = util.make_temp_name('em_list')
em_list = pyrsistence.EMList(dirname)
for i in util.xrange(0x1000000):
em_list.append(i)
t2 = time.time()
util.msg('Done in %d sec.' % (t2 - t1))
# Close and remove external memory list from disk.
em_list.close()
shutil.rmtree(dirname)
return 0
def main(argv):
# Initialize new external memory dictionary.
util.msg('Populating external memory dictionary')
t1 = time.time()
dirname = util.make_temp_name('em_dict')
em_dict = pyrsistence.EMDict(dirname)
for i in util.xrange(0x1000000):
em_dict[i] = i
t2 = time.time()
util.msg('Done in %d sec.' % (t2 - t1))
# Close and remove external memory dictionary from disk.
em_dict.close()
shutil.rmtree(dirname)
return 0
def __str__(self):
"""
The str(Reader) is intended for debugging.
"""
return msg("""
LineReader
cur[%3d] = %s
start = %d
stop = %d
linenr = %d
eof = %s
""" % (len(self.cur), self.cur[:72],
self.start, self.stop, self.linenr, self.eof))
def getPropertyEntryContent(self):
"""
Parses property entry of the form:
chararcter space n:integer newline bytes[n] newline
and returns the bytes[n].
"""
assert (len(self.reader.cur) and
self.reader.cur[0:2] in ['K ', 'V ', 'D ']), msg("""
Expected a pair of property entry lines, where the
first has the form (K|V|D) <number>. Found this:
%s""" % (self.reader,))
n = int(self.reader.cur[2:])
self.reader.next()
result = self.getBytes(n)
return result
def browser(opt, url):
# what os?
if sys.platform=='darwin':
cmd = 'sleep 1; open -a "Google Chrome" "%s"' % url
elif sys.platform=='linux2':
cmd = 'sleep 1; google-chrome "%s" &' % url
elif sys.platform=='win32':
cmd = 'timeout 2 && start /b chrome "%s" &' % url
else:
raise Exception('unknown platform ' + sys.platform)
# launch it
if cmd:
util.msg('opening a browser window on', url)
rc = subprocess.call(cmd, shell=True)
if rc != 0:
util.msg('can\'t open browser; is Google Chrome installed?')
else:
util.msg('don\'t know how to open a browser on your platform')
# go into background
# not as robust as daemonizing, but that's not needed, and adds an external dependency
if not opt.nofork:
log_fn = 'timeseries.%d.log' % opt.port
util.msg('going into background; sending output to ' + log_fn)
util.msg('will terminate when browser window closes')
util.msg('use --nofork to run in foreground')
if os.fork():
os._exit(0)
sys.stdin.close()
sys.stderr = sys.stdout = open(log_fn, 'a')
util.msg('\n===', url)
signal.signal(signal.SIGHUP, signal.SIG_IGN)
module[task['module']].exploit(task['request'])
self.work_queue.task_done()
except Exception, e:
#print str(e)
break
if __name__ == '__main__':
O = {}
NODE_KEY = "a88b92531ba974f68bc1fd5938fc77"
NODE_DEBUG = 0
SERVER = "http://w/uauc/playweb/"
util.msg("PlayWeb Node 1.0")
util.msg("Server:%s Key:%s Debug:%d" % (SERVER, NODE_KEY, NODE_DEBUG))
util.msg("Listening server project...")
while 1:
r = util.http_get(SERVER + "/index.php?m=node&a=get_task")
if r['data'] != " " :
O = eval(util.decode_str(r['data'], NODE_KEY))
break
time.sleep(1)
O['debug'] = NODE_DEBUG
util.msg("[Project] Target:%s Time:%s Module:%s Thread:%s" % (O['target'], util.date(O['start_time']), O['module'], O['thread']), 1)
O['target'] = "w"
O['key'] = NODE_KEY
#O['depth'] = 5 # notice
O['server_url'] = SERVER + "?m=node&a="
O['web-ports'] = util.csv2array(O['web-ports'])
def do_GET(self):
# parse command-line args passed in url query string as an 'args' parameter
def query2opt(query):
args = shlex.split(query['args'][0])
return __main__.get_opt(args)
# parse url, extracting path and query portions
_, _, path, _, query, _ = urlparse.urlparse(self.path)
query = urlparse.parse_qs(query)
# query to root is redirected to default session 0
if path=='/':
self.send_response(301) # permanent
self.send_header('Location', '/0')
# open a new view in a new window
# expects command-line arg string in url parameter "args"
# parse off the query, open new session based on that, then redirect to bare session url
elif path=='/open':
opt = query2opt(query) # parse url "args" parameter
ses = Ses(opt, server=True) # new session
self.send_response(302) # temporary redirect
self.send_header('Location', ses.path)
# top-level page: return the container, which includes
# progress message area - loaded via /ses/progress url in progress phase (below)
# content area - loaded via /ses/content url in content phase (below)
elif path in Ses.sessions:
ses = Ses.sessions[path]
self.prepare(ses)
html.container(ses)
# info for a given time t
elif path.endswith('/info'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
t = float(query['t'][0])
self.prepare(ses)
html.info(ses, t)
# raw info for a given time t
elif path.endswith('/raw'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
t = float(query['t'][0])
self.prepare(ses)
html.raw(ses, t, kind='raw')
elif path.endswith('/metadata'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
t = float(query['t'][0])
self.prepare(ses)
html.raw(ses, t, kind='metadata')
# progress phase: load the data in preparation for generating content
# while emitting progress messages. We also accept new view parameters to open
# new view in current window as command-line arg string in url parameter "args"
elif path.endswith('/progress'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
if 'args' in query:
ses.opt = query2opt(query) # parse url "args" parameter
self.prepare(ses)
html.load(ses)
# content phase: generate actual html view from graph data loadedin progress phase
elif path.endswith('/content'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
self.prepare(ses)
html.page(ses)
# a window closed
elif '/close/' in path:
if Handler.exit_on_close:
path, _, what = path.rsplit('/', 2)
util.msg('closing', path, '('+what+')')
if path in Ses.sessions:
del Ses.sessions[path]
if not Ses.sessions:
util.msg('all sessions closed, exiting')
os._exit(0)
# otherwise not found
else:
self.send_response(404) # not found
def error(self, p):
if not p:
util.msg('parse error: unexpected EOF')
else:
util.msg(f'parse error: {p}')
def verify_backups(self, only='') -> None:
"""Verify all, or only the latest, backup(s) in this repository.
Iterate through every 'new' and 'old' entry in every (or latest)
backup, and verify that (1) the hash exists, and (2) its contents
matches its name.
"""
if only == '':
bkup_list = self.all_backups
else:
bkup_list = [only]
num_backups = len(bkup_list)
# entries = 0
num_files = 0
hits = 0
all_hashes: Set[str] = set()
good: Set[str] = set()
bad: Set[str] = set()
missing: Set[str] = set()
for b in bkup_list:
util.msg(f'Checking: {b}')
bkup = os.path.join(self.backups, b)
with open(bkup, 'rt') as f:
line_num = 0
saw_end = False
for line in f:
line_num += 1
if line_num == 1 and not line.startswith('start'):
util.fatal(f'Backup {bkup} corrupted. No start.')
if line[0:3] in ('new', 'old'):
num_files += 1
flds = line.split('\t')
h = flds[1]
this_file = flds[3]
all_hashes.add(h)
if h in good:
hits += 1
# continue
elif h in bad:
hits += 1
util.error(f'invalid hash {h} for {this_file}')
# continue
else:
# We haven't seen this hash before
(d, ff) = self.fname_from_hash(h)
if self.find_file(os.path.join(d, ff)):
if _verify_hash(os.path.join(self.objects, d),
ff):
good.add(h)
else:
bad.add(h)
t = this_file
util.error(f'invalid hash {h} for {t}')
else:
missing.add(h)
util.error(f'missing {h} for {this_file}')
else:
# print(line_num, line)
# This should be a trailer line
if line.startswith('end'):
saw_end = True
if not saw_end:
util.warning(f'Backup {bkup} has no end marker')
if len(all_hashes) != len(good) + len(bad) + len(missing):
util.fatal(f'hash bug: {len(all_hashes)} \
{len(good)} {len(bad)} {len(missing)}')
util.msg('Verify results:')
util.msg(f'backups checked = {num_backups}')
util.msg(f'files checked = {num_files}')
util.msg(f'invalid = {len(bad)}')
util.msg(f'missing = {len(missing)}')
util.msg(f'cache hits = {hits}')
def main():
parser = argparse.ArgumentParser(description="")
parser.add_argument(
"alignment", help="Fasta format alignment of sequences to be analysed")
parser.add_argument("width", help="Width of nucleotide window to analyse")
parser.add_argument(
"run_id",
help=
"Identifier for this run, to be used as a key for joining datatables")
parser.add_argument("-p",
help="Overlap proportions for windows",
nargs="+",
default=[])
parser.add_argument("-wd", help="Working directory", default=None)
args = parser.parse_args()
if args.wd == None:
WD = os.getcwd() + "/"
else:
raise ValueError("User specified working directory not implemented!")
#if os.path.exists(args.wd): WD = args.wd
#else: raise ValueError("Working directory path does not exist")
W = int(args.width)
try:
user_p_fractions = [float(x) for x in args.p]
except ValueError:
print "Error: Overlap proportion arguments must be numerical values, separated by space character"
exit()
if len(user_p_fractions) > util.MAX_P_FRACS:
raise ValueError("Error: Maximum of %d user-defined window shifts" %
util.MAX_P_FRACS)
p_fractions = [0.0] + user_p_fractions
colours = dict(zip(p_fractions,
util.COLOURS)) # colours used for p fractions in plot
sequences = reader.ReadInFasta(args.alignment)
util.init_msg("motif_pattern='%s'" % util.MOTIF)
util.init_msg("stem_loop_pattern='%s'" % util.STEM_LOOP_PATTERN)
# NB for current setup to work, the ref seq needs to be the longest seq.
# sites not found in the ref seq can't be described for others
reference_seq = sequences[0][1] # expecting this will include gaps
ref_unalign_indices = util.unalign_indices(
reference_seq) # indices for reference sequence unaligned
ref_unalign_len = max(
ref_unalign_indices) # assuming first seq in file is the reference
util.init_msg("width=%d" % W)
align_len = len(
reference_seq) # assuming aligned properly and all the same length
check_names_length(
[pair[0] for pair in sequences], align_len
) # most unaligned sequences will have length less than align_len, but this is the max length possible
util.init_msg("aln_length=%d" % align_len)
SEQ_NAME_DELIM = "."
HEAD = "HEADER_"
TAG_SEQ = "SEQ:"
TAG_WIN = "WIN:"
TAG_STRUCT = "STRUCT:"
TAG_LOOP = "SL:"
print util.tabmsg([HEAD + TAG_SEQ, "run_id", "seq_id", "group", "length"])
print util.tabmsg([
HEAD + TAG_WIN, "run_id", "win_id", "seq_id", "shift", "start_a",
"end_a", "start_u", "end_u", "has_motif"
])
print util.tabmsg([
HEAD + TAG_STRUCT, "run_id", "struct_id", "seq_id", "win_id",
"struct_number", "s_energy", "dotbracket"
])
print util.tabmsg([
HEAD + TAG_LOOP, "run_id", "loop_id", "seq_id", "win_id", "struct_id",
"loop_number", "start_a", "end_a", "start_u", "end_u"
])
win_id, struct_id, loop_id = (0, 0, 0)
run_id = args.run_id # NB remains string
print "run_id:\t%s" % run_id
# do analysis
for nameSeqPair in sequences:
genome_with_gaps = nameSeqPair[1].upper().replace("T", "U")
unalign_indices = util.unalign_indices(genome_with_gaps)
genome = genome_with_gaps.replace(util.GAP, "")
group, seq_id = nameSeqPair[0].split(
SEQ_NAME_DELIM) # assuming name is in format GROUP.SEQ_ID
L = len(genome)
#util.init_msg("sequence=%s, unalign_length=%d" % (seq_id, L))
print util.tabmsg([TAG_SEQ, run_id, seq_id, group, L])
for P in p_fractions:
util.init_msg("shift=%.2f" % P)
check_window_parameters(W, P)
windows = get_windows(L, W, P)
for window in windows:
util.init_msg(
"windows:%d.%d" % (window[0] + 1, window[1])
) # correct for zero based. Don't +1 for end so numbers are inclusive
windows_sanity_check(windows, genome)
for window in windows:
win_start_u, win_end_u = window # unaligned numbers. NB indices are like slice numbers (upper is exclusive)
win_start_a, win_end_a = unalign_indices.index(
win_start_u
), unalign_indices.index(win_end_u - 1) + 1 # aligned numbers
analysis_id = ".".join(
[seq_id, str(win_start_u + 1),
str(win_end_u)]
) # +1 to correct for zero based, and don't -1 for win_end_u for the same reason
win_seq = genome[win_start_u:win_end_u]
has_motif = pattern.has_motif(win_seq)
print util.tabmsg([
TAG_WIN, run_id, win_id, seq_id, P, win_start_a, win_end_a,
win_start_u, win_end_u, has_motif
])
#util.msg(analysis_id, "seq:"+win_seq)
if has_motif:
util.msg(analysis_id, "contains motif, estimating SS")
seq_structs = ss_prediction.predict_ss(
win_seq, analysis_id,
WD) # will return empty list if no .ct file available
util.msg(analysis_id, "%d SS produced" % len(seq_structs))
for iSeqStruct in range(len(seq_structs)):
print util.tabmsg([
TAG_STRUCT, run_id, struct_id, seq_id, win_id,
iSeqStruct + 1, seq_structs[iSeqStruct].dG,
seq_structs[iSeqStruct].ss
])
motif_loops = pattern.find_motif_loops(
seq_structs[iSeqStruct]
) # list of subsequence indices for stem loops containing pattern in this ss
if len(motif_loops) == 0:
util.msg(
analysis_id, "SS_%d does NOT have loop_motif" %
(iSeqStruct + 1))
else:
util.msg(
analysis_id,
"SS_%d DOES have %d motif_loop(s):" %
(iSeqStruct + 1, len(motif_loops)))
util.result_msg(seq_structs[iSeqStruct]
) # print the whole SeqStruct
for iLoop in range(
len(motif_loops)
): # NB motif_loop indices are like slices: start is inclusive, end is exclusive
loop_start_u, loop_end_u = motif_loops[iLoop][
0] + win_start_u, motif_loops[iLoop][
1] + win_start_u # _u meaning unaligned
loop_start_a, loop_end_a = unalign_indices.index(
loop_start_u), unalign_indices.index(
loop_end_u)
print util.tabmsg([
TAG_LOOP, run_id, loop_id, seq_id, win_id,
struct_id, iLoop + 1, loop_start_a,
loop_end_a, loop_start_u, loop_end_u
])
#loop_id = ".".join([analysis_id, str(iSeqStruct+1), str(iLoop+1)])
#stem_loop_seq = win_seq[motif_loops[iLoop][0]:motif_loops[iLoop][1]]
# for loop_start_u/loop_end_u, +1 correct for zero based for start. Not +1 for end because index value is exclusive
#util.indx_msg("U", loop_id, P, (loop_start_u+1), loop_end_u, stem_loop_seq) # this seq's indices
#util.indx_msg("A", loop_id, P, (loop_start_a+1), loop_end_a, stem_loop_seq) # the ref seq's indices
loop_id += 1
struct_id += 1
else: # if has motif
util.msg(analysis_id, "no motif in this window")
win_id += 1
print "End of analysis"
def cmd_configure(ctx, config):
srcnode = ctx.srcnode.abspath()
bldnode = ctx.bldnode.abspath()
ctx.load('waf', tooldir='pylib/')
ctx.load('waf_unit_test')
from pylib.util import parse_version
parse_version(config)
ctx.env.NTPS_RELEASE = config["NTPS_RELEASE"]
ctx.env.NTPS_VERSION_MAJOR = config["NTPS_VERSION_MAJOR"]
ctx.env.NTPS_VERSION_MINOR = config["NTPS_VERSION_MINOR"]
ctx.env.NTPS_VERSION_REV = config["NTPS_VERSION_REV"]
ctx.env.NTPS_VERSION = "%s.%s.%s" % (ctx.env.NTPS_VERSION_MAJOR, ctx.env.NTPS_VERSION_MINOR, ctx.env.NTPS_VERSION_REV)
ctx.define("NTPS_VERSION_MAJOR", ctx.env.NTPS_VERSION_MAJOR, comment="Major version number")
ctx.define("NTPS_VERSION_MINOR", ctx.env.NTPS_VERSION_MINOR, comment="Minor version number")
ctx.define("NTPS_VERSION_REV", ctx.env.NTPS_VERSION_REV, comment="Revision version number")
ctx.env.OPT_STORE = config["OPT_STORE"]
opt_map = {}
# Wipe out and override flags with those from the commandline
for flag in ctx.env.OPT_STORE:
opt = flag.replace("--", "").upper() # XXX: find a better way.
opt_map[opt] = ctx.env.OPT_STORE[flag]
msg("--- Configuring host ---")
ctx.setenv('host', ctx.env.derive())
ctx.load('compiler_c')
if not ctx.env.NTPS_RELEASE:
ctx.load('bison')
for opt in opt_map:
ctx.env[opt] = opt_map[opt]
from compiler import check_compiler
check_compiler(ctx)
if ctx.options.enable_rtems_trace:
ctx.find_program("rtems-tld", var="BIN_RTEMS_TLD", path_list=[ctx.options.rtems_trace_path, ctx.env.BINDIR])
ctx.env.RTEMS_TEST_ENABLE = True
ctx.env.RTEMS_TEST_FLAGS = ["-C", "%s/devel/trace/ntpsec-trace.ini" % srcnode,
"-W", "%s/ntpsec-wrapper" % bldnode,
"-P", "%s/devel/trace/" % srcnode,
"-f", "-I%s" % bldnode,
"-f", "-I%s/include/" % srcnode,
"-f", "-I%s/libisc/include/" % srcnode,
"-f", "-I%s/libisc/unix/include/" % srcnode]
# Not needed to build. Used by utility scripts.
ctx.find_program("awk", var="BIN_AWK", mandatory=False)
ctx.find_program("perl", var="BIN_PERL", mandatory=False)
ctx.find_program("sh", var="BIN_SH", mandatory=False)
# used to make man and html pages
ctx.find_program("asciidoc", var="BIN_ASCIIDOC", mandatory=False)
ctx.find_program("a2x", var="BIN_A2X", mandatory=False)
ctx.find_program("xsltproc", var="BIN_XSLTPROC", mandatory=False)
ctx.env.ENABLE_DOC = False
if ctx.env.BIN_ASCIIDOC and ctx.env.BIN_XSLTPROC and ctx.env.BIN_A2X:
ctx.env.ENABLE_DOC = True
if (ctx.options.enable_doc or ctx.options.enable_doc_only) and not ctx.env.ENABLE_DOC:
ctx.fatal("asciidoc and xsltproc are required in order to build documentation")
elif (ctx.options.enable_doc or ctx.options.enable_doc_only):
ctx.env.ASCIIDOC_FLAGS = ["-f", "%s/docs/asciidoc.conf" % ctx.srcnode.abspath()]
ctx.env.ENABLE_DOC_ONLY = ctx.options.enable_doc_only
ctx.env.ENABLE_DOC_USER = ctx.options.enable_doc
ctx.env.PATH_DOC = ctx.options.path_doc
# XXX: conditionally build this with --disable-man? Should it build without docs enabled?
ctx.env.A2X_FLAGS = ["--format", "manpage", "--asciidoc-opts=--conf-file=%s/docs/asciidoc.conf" % ctx.srcnode.abspath()]
if not ctx.options.enable_a2x_xmllint:
ctx.env.A2X_FLAGS += ["--no-xmllint"]
# Disable manpages within build()
if ctx.options.disable_manpage:
ctx.env.DISABLE_MANPAGE = True
from os.path import exists
from waflib.Utils import subprocess
if exists(".git") and ctx.find_program("git", var="BIN_GIT", mandatory=False):
ctx.start_msg("DEVEL: Getting revision")
cmd = ["git", "log", "-1", "--format=%H"]
p = subprocess.Popen(cmd, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=None)
ctx.env.NTPS_REVISION, stderr = p.communicate()
ctx.env.NTPS_REVISION = ctx.env.NTPS_REVISION.replace("\n", "")
ctx.end_msg(ctx.env.NTPS_REVISION)
ctx.start_msg("Building version")
ctx.env.NTPS_VERSION_STRING = ctx.env.NTPS_VERSION
if ctx.env.NTPS_REVISION:
ctx.env.NTPS_VERSION_STRING += "-%s" % ctx.env.NTPS_REVISION[:7]
if ctx.options.build_version_tag:
ctx.env.NTPS_VERSION_STRING += "-%s" % ctx.options.build_version_tag
ctx.define("NTPS_VERSION_STRING", ctx.env.NTPS_VERSION_STRING)
ctx.end_msg(ctx.env.NTPS_VERSION_STRING)
msg("--- Configuring main ---")
ctx.setenv("main", ctx.env.derive())
# XXX: temp hack to fix --enable-doc-only
ctx.env.ENABLE_DOC_ONLY = ctx.options.enable_doc_only
# The rest is not needed for documentation building.
if ctx.options.enable_doc_only:
return
from check_type import check_type
from check_sizeof import check_sizeof
from check_structfield import check_structfield
for opt in opt_map:
ctx.env[opt] = opt_map[opt]
if ctx.options.cross_compiler:
ctx.env.ENABLE_CROSS = True
ctx.start_msg("Using Cross compiler CC:")
# ctx.get_cc_version(ctx.env.CC, gcc=True)
ctx.end_msg(ctx.options.cross_compiler)
ctx.env.CC = [ctx.options.cross_compiler]
ctx.env.LINK_CC = [ctx.options.cross_compiler]
if ctx.env["CROSS-CFLAGS"]:
ctx.env.CFLAGS = opt_map["CROSS-CFLAGS"]
if ctx.env["CROSS-LDFLAGS"]:
ctx.env.LDFLAGS = opt_map["CROSS-LDFLAGS"]
if ctx.options.list:
from refclock import refclock_map
print "ID Description"
print "~~ ~~~~~~~~~~~"
for id in refclock_map:
print "%-5s %s" % (id, refclock_map[id]["descr"])
return
# This needs to be at the top since it modifies CC and AR
if ctx.options.enable_fortify:
from check_fortify import check_fortify
check_fortify(ctx)
if ctx.options.enable_debug_gdb:
ctx.env.CFLAGS += ["-g"]
if ctx.options.enable_saveconfig:
ctx.define("SAVECONFIG", 1)
if not ctx.options.disable_debug:
ctx.define("DEBUG", 1, comment="Enable debug mode")
ctx.env.BISONFLAGS += ["--debug"]
ctx.env.CFLAGS += ["-Wall", "-Wextra"] # Default CFLAGS.
# Check target platform.
ctx.start_msg("Checking build target")
from sys import platform
if platform == "win32":
ctx.env.PLATFORM_TARGET = "win"
elif platform == "darwin":
ctx.env.PLATFORM_TARGET = "osx"
elif platform.startswith("freebsd"):
ctx.env.PLATFORM_TARGET = "freebsd"
elif platform.startswith("netbsd"):
ctx.env.PLATFORM_TARGET = "netbsd"
elif platform.startswith("openbsd"):
ctx.env.PLATFORM_TARGET = "openbsd"
else:
ctx.env.PLATFORM_TARGET = "unix"
ctx.end_msg(ctx.env.PLATFORM_TARGET )
ctx.define("PLATFORM_%s" % ctx.env.PLATFORM_TARGET.upper(), 1, comment="Operating system detected by Python (%s)" % platform)
# XXX: hack
if ctx.env.PLATFORM_TARGET in ["freebsd", "osx", "openbsd"]:
ctx.env.PLATFORM_INCLUDES = ["/usr/local/include"]
ctx.env.PLATFORM_LIBPATH = ["/usr/local/lib"]
elif ctx.env.PLATFORM_TARGET == "netbsd":
ctx.env.PLATFORM_LIBPATH = ["/usr/lib"]
elif ctx.env.PLATFORM_TARGET == "win":
ctx.load("msvc")
# OS X needs this for IPv6
if ctx.env.PLATFORM_TARGET == "osx":
ctx.define("__APPLE_USE_RFC_3542", 1, comment="Needed for IPv6 support")
# int32_t and uint32_t probes aren't really needed, POSIX guarantees
# them. But int64_t and uint64_t are not guaranteed to exist on 32-bit
# machines.
# Used by timevalops and timespecops in tests/libntp/
# May go away when that is cleaned up.
types = ["uint64_t"]
for inttype in sorted(types):
ctx.check_type(inttype, ["stdint.h", "sys/types.h"])
net_types = (
("struct if_laddrconf", ["sys/types.h", "net/if6.h"]),
("struct if_laddrreq", ["sys/types.h", "net/if6.h"]),
)
for (f, h) in net_types:
ctx.check_type(f, h)
structures = (
("struct timex", ["sys/time.h", "sys/timex.h"]),
("struct ntptimeval", ["sys/time.h", "sys/timex.h"]),
)
for (s, h) in structures:
ctx.check_type(s, h)
structure_fields = (
("time_tick", "timex", ["sys/time.h", "sys/timex.h"]),
("modes", "timex", ["sys/time.h", "sys/timex.h"]),
("time.tv_nsec", "ntptimeval", ["sys/time.h", "sys/timex.h"]),
)
for (f, s, h) in structure_fields:
ctx.check_structfield(f, s, h)
# mostly used by timetoa.h and timespecops.h
sizeofs = [
("time.h", "time_t"),
(None, "int"),
(None, "long"),
(None, "long long"),
]
for header, sizeof in sorted(sizeofs):
ctx.check_sizeof(header, sizeof)
# The protocol major number
ctx.define("NTP_API", 4, comment="Protocol major number.")
ctx.define("NTP_KEYSDIR", "%s/etc" % ctx.env.PREFIX, comment="NTP key file directory")
ctx.define("GETSOCKNAME_SOCKLEN_TYPE", "socklen_t", quote=False, comment="socklen type")
ctx.define("DFLT_RLIMIT_STACK", 50, comment="Default stack size")
ctx.define("DFLT_RLIMIT_MEMLOCK", 32, comment="Locked memory size")
probe_multicast(ctx, "MCAST", "Checking for multicast capability")
ctx.define("TYPEOF_IP_MULTICAST_LOOP", "u_char", quote=False, comment="Multicast loop type") #XXX: check for mcast type
# These are helpful and don't break Linux or *BSD
ctx.define("OPEN_BCAST_SOCKET", 1, comment="Whether to open a broadcast socket")
ctx.define("HAS_ROUTING_SOCKET", 1, comment="Whether a routing socket exists")
ctx.check_cc(lib="edit", mandatory=False, comment="libedit library")
ctx.check_cc(lib="m", comment="Math library")
ctx.check_cc(lib="ossaudio", mandatory=False, comment="ossaudio for NetBSD") # NetBSD audio
ctx.check_cc(lib="rt", mandatory=False, comment="realtime library")
ctx.check_cc(lib="curses", mandatory=False, comment="curses library, required for readline on OpenBSD") # Required for readline on OpenBSD.
ctx.check_cc(lib="readline", use="CURSES", mandatory=False, comment="readline library")
ctx.check_cc(lib="gcc_s", mandatory=False, comment="GCC runtime library.")
# Find OpenSSL. Must happen before function checks
if ctx.options.enable_crypto:
from check_openssl import configure_ssl
configure_ssl(ctx)
# Optional functions. Do all function checks here, otherwise
# we're likely to duplicate them.
functions = (
('adjtimex', ["sys/time.h", "sys/timex.h"]),
('closefrom', ["stdlib.h"]),
('clock_gettime', ["time.h"], "RT"),
('clock_settime', ["time.h"], "RT"),
('EVP_MD_do_all_sorted', ["openssl/evp.h"], "CRYPTO"),
('getclock', ["sys/timers.h"]),
('getpassphrase', ["stdlib.h"]), # Sun systems
('MD5Init', ["md5.h"], "CRYPTO"),
('ntp_adjtime', ["sys/time.h", "sys/timex.h"]), # BSD
('ntp_gettime', ["sys/time.h", "sys/timex.h"]), # BSD
('res_init', ["resolv.h"]),
("rtprio", ["sys/rtprio.h"]), # Sun/BSD
('sched_setscheduler', ["sched.h"]),
('settimeofday', ["sys/time.h"], "RT"), # BSD
('strlcpy', ["string.h"]),
('strlcat', ["string.h"]),
('timer_create', ["time.h"])
)
for ft in functions:
if len(ft) == 2:
probe_function_with_prerequisites(ctx, function=ft[0],
prerequisites=ft[1])
else:
probe_function_with_prerequisites(ctx, function=ft[0],
prerequisites=ft[1],
use=ft[2])
# Nobody uses the symbol, but this seems like a good sanity check.
ctx.check_cc(header_name="stdbool.h", mandatory=True, comment="Sanity check.")
# This is a list of every optional include header in the
# codebase that is guarded by a directly corresponding HAVE_*_H symbol.
#
# In some cases one HAVE symbol controls inclusion of more than one
# header; there is an example of this in ntp/audio.c. In these cases
# only the one header name matching the pattern of the HAVE_*_H symbol
# name is listed here, so we can invert the relationship to generate
# tests for all the symbols.
#
# Some of these are cruft from ancient big-iron systems and should
# be removed.
optional_headers = (
"dns_sd.h", # NetBSD, Apple, mDNS
"histedit.h", # Apple
("ifaddrs.h", ["sys/types.h"]),
"libscf.h", # Solaris
"linux/if_addr.h",
"linux/rtnetlink.h",
"linux/serial.h",
#"linux/seccomp.h", - Doesn't build yet, investigate
"machine/soundcard.h",
("md5.h", ["sys/types.h"]),
"net/if6.h",
("net/route.h", ["sys/types.h","sys/socket.h","net/if.h"]),
"netinfo/ni.h", # Apple
"priv.h", # Solaris
("readline/readline.h",["stdio.h"]),
("readline/history.h", ["stdio.h","readline/readline.h"]),
("resolv.h", ["sys/types.h","netinet/in.h","arpa/nameser.h"]),
"semaphore.h",
"stdatomic.h",
"sys/audioio.h",
"sys/capability.h", # Linux
"sys/ioctl.h",
"sys/modem.h", # Apple
"sys/prctl.h", # Linux
"sys/sockio.h",
"sys/soundcard.h",
("sys/sysctl.h", ["sys/types.h"]),
("timepps.h", ["inttypes.h"]),
("sys/timepps.h", ["inttypes.h", "sys/time.h"]),
"utmpx.h", # missing on RTEMS and OpenBSD
("sys/timex.h", ["sys/time.h"]),
"sys/audio.h"
)
for hdr in optional_headers:
if type(hdr) == type(""):
if ctx.check_cc(header_name=hdr, mandatory=False, comment="<%s> header" % hdr):
continue
else:
(hdr, prereqs) = hdr
if probe_header_with_prerequisites(ctx, hdr, prereqs):
continue
if os.path.exists("/usr/include/" + hdr):
# Sanity check...
print "Compilation check failed but include exists %s" % hdr
if ctx.get_define("HAVE_TIMEPPS_H") or ctx.get_define("HAVE_SYS_TIMEPPS_H"):
ctx.define("HAVE_PPSAPI", 1, comment="Enable the PPS API")
# Check for Solaris capabilities
if ctx.get_define("HAVE_PRIV_H") and sys.platform == "Solaris":
ctx.define("HAVE_SOLARIS_PRIVS", 1, comment="Enable Solaris Privileges (Solaris only)")
from check_sockaddr import check_sockaddr
check_sockaddr(ctx)
# Some systems don't have sys/timex.h eg OS X, OpenBSD...
if ctx.get_define("HAVE_SYS_TIMEX_H"):
ctx.env.HEADER_SYS_TIMEX_H = True
# Some systems don't have sys/audio.h eg OS X, OpenBSD...
if ctx.get_define("HAVE_SYS_AUDIO_H") or \
ctx.get_define("HAVE_SYS_SOUNDCARD_H") or \
ctx.get_define("HAVE_MACHINE_SOUNDCARD_H"):
ctx.env.HAVE_AUDIO = True # makes util/tg2
if ctx.options.refclocks:
from refclock import refclock_config
# Enable audio when the right headers exist.
if ctx.get_define("HAVE_SYS_AUDIOIO_H") or \
ctx.get_define("HAVE_SYS_SOUNDCARD_H") or \
ctx.get_define("HAVE_MACHINE_SOUNDCARD_H"):
ctx.env.AUDIO_ENABLE = True
refclock_config(ctx)
# NetBSD (used to) need to recreate sockets on changed routing.
# Perhaps it still does. If so, this should be set. The autoconf
# build set it "if the OS clears cached routes when more specifics
# become available".
# ctx.define("OS_MISSES_SPECIFIC_ROUTE_UPDATES", 1)
if ctx.options.enable_leap_smear:
ctx.define("ENABLE_LEAP_SMEAR", 1, comment="Enable experimental leap smearing code")
if ctx.options.enable_mssntp:
ctx.define("ENABLE_MSSNTP", 1, comment="Enable MS-SNTP extensions https://msdn.microsoft.com/en-us/library/cc212930.aspx")
if ctx.options.enable_lockclock:
ctx.define("ENABLE_LOCKCLOCK", 1, comment="Enable NIST 'lockclock'")
if not ctx.options.disable_droproot:
ctx.define("ENABLE_DROPROOT", 1, comment="Drop root after initialising")
if not ctx.options.disable_dns_lookup:
ctx.define("ENABLE_DNS_LOOKUP", 1, comment="Enable DNS lookup of hostnames")
if not ctx.options.disable_dns_retry:
ctx.define("ENABLE_DNS_RETRY", 1, comment="Retry DNS lookups after an initial failure")
# There is an ENABLE_ASYMMETRIC that enables a section of the
# protocol code having to do with handling very long asymmetric
# delays, as in space communications. Likely this code has never
# been enabled for production.
# Won't be true under Windows, but is under every Unix-like OS.
ctx.define("HAVE_WORKING_FORK", 1, comment="Whether a working fork() exists")
# Does the kernel implement a phase-locked loop for timing?
# All modern Unixes (in particular Linux and *BSD have this).
#
# The README for the (now deleted) kernel directory says this:
# "If the precision-time kernel (KERNEL_PLL define) is
# configured, the installation process requires the header
# file /usr/include/sys/timex.h for the particular
# architecture to be in place."
#
if ctx.get_define("HAVE_SYS_TIMEX_H"):
ctx.define("HAVE_KERNEL_PLL", 1, comment="Whether phase-locked loop for timing exists")
# SO_REUSEADDR socket option is needed to open a socket on an
# interface when the port number is already in use on another
# interface. Linux needs this, NetBSD does not, status on
# other platforms is unknown. It is probably harmless to
# have it on everywhere.
ctx.define("NEED_REUSEADDR_FOR_IFADDRBIND", 1, comment="Whether SO_REUSEADDR is needed to open same sockets on alternate interfaces, required by Linux at least")
# Not yet known how to detect HP-UX at version < 8, but that needs this.
# Shouldn't be an issue as 8.x shipped in January 1991!
# ctx.define("NEED_RCVBUF_SLOP", 1)
# It should be possible to use asynchrpnous I/O with notification
# by SIGIO on any Unix conformant to POSIX.1-2001. But the code to
# do this is untested and there are historical reasons to suspect
# it might not work reliably on all platforms. Enable cautiously
# and test carefully.
# ctx.define("ENABLE_SIGNALED_IO", 1)
# Used in libntp/audio.c:
# [[
# #ifdef HAVE_MACHINE_SOUNDCARD_H
# # include <machine/soundcard.h>
# #endif
# #ifdef HAVE_SYS_SOUNDCARD_H
# # include <sys/soundcard.h>
# #endif
# ]],
# [[
# extern struct snd_size *ss;
# return ss->rec_size;
# ]]
# ctx.define("HAVE_STRUCT_SND_SIZE", 1)
# These are required by the SHA2 code and various refclocks
if sys.byteorder == "little":
pass
elif sys.byteorder == "big":
ctx.define("WORDS_BIGENDIAN", 1)
else:
print "Can't determine byte order!"
probe_vsprintfm(ctx, "VSNPRINTF_PERCENT_M",
"Checking for %m expansion in vsnprintf(3)")
# Define CFLAGS/LDCFLAGS for -vv support.
ctx.define("NTPS_CFLAGS", " ".join(ctx.env.CFLAGS).replace("\"", "\\\""), comment="CFLAGS used when compiled")
ctx.define("NTPS_LDFLAGS", " ".join(ctx.env.LDFLAGS).replace("\"", "\\\""), comment="LDFLAGS used when compiled")
# Check for directory separator
if ctx.env.PLATFORM_TARGET == "win":
sep = "\\"
else:
sep = "/"
ctx.define("DIR_SEP", "'%s'" % sep, quote=False, comment="Directory separator used")
# libisc/
# XXX: Hack that needs to be fixed properly for all platforms
ctx.define("ISC_PLATFORM_NORETURN_PRE", "", quote=False)
ctx.define("ISC_PLATFORM_NORETURN_POST", "__attribute__((__noreturn__))", quote=False)
ctx.define("ISC_PLATFORM_HAVEIFNAMETOINDEX", 1)
ctx.define("ISC_PLATFORM_HAVEIN6PKTINFO", 1)
ctx.define("ISC_PLATFORM_HAVEIPV6", 1)
ctx.define("ISC_PLATFORM_HAVESCOPEID", 1)
if ctx.get_define("HAVE_SYS_SYSCTL_H"):
ctx.define("HAVE_IFLIST_SYSCTL", 1, comment="Whether sysctl interface exists")
# Header checks
from pylib.check_cap import check_cap_header
check_cap_header(ctx)
from pylib.check_libevent2 import check_libevent2_header
check_libevent2_header(ctx)
from pylib.check_pthread import check_pthread_header_lib
check_pthread_header_lib(ctx)
if not ctx.options.disable_mdns_registration:
from pylib.check_mdns import check_mdns_header
check_mdns_header(ctx)
# Run checks
from pylib.check_cap import check_cap_run
check_cap_run(ctx)
from pylib.check_libevent2 import check_libevent2_run
check_libevent2_run(ctx)
from pylib.check_pthread import check_pthread_run
check_pthread_run(ctx)
if not ctx.options.disable_mdns_registration:
from pylib.check_mdns import check_mdns_run
check_mdns_run(ctx)
if ctx.env.PTHREAD_ENABLE:
ctx.define("ISC_PLATFORM_USETHREADS", 1)
ctx.start_msg("Writing configuration header:")
ctx.write_config_header("config.h")
ctx.end_msg("config.h", "PINK")
def yesno(x):
if x:
return "Yes"
return "No"
msg("")
msg("Build Options")
msg_setting("CC", " ".join(ctx.env.CC))
msg_setting("CFLAGS", " ".join(ctx.env.CFLAGS))
msg_setting("LDFLAGS", " ".join(ctx.env.LDFLAGS))
msg_setting("PREFIX", ctx.env.PREFIX)
msg_setting("Debug Support", yesno(not ctx.options.disable_debug))
msg_setting("Refclocks", ", ".join(ctx.env.REFCLOCK_LIST))
msg_setting("Build Manpages", yesno(ctx.env.ENABLE_DOC and not ctx.env.DISABLE_MANPAGE))
if ctx.options.enable_debug:
msg("")
msg("*** --enable-debug ignored. (default on now)")
msg("")
def parseNode(self):
"""
Parse a single node, which may contain both UserProperties and
TextContent.
Node =
BeginNode
BlankLine?
UserProperties?
(
TextContent
BlankLine
)?
"""
chunk_pos = self.reader.start
dump_props = BeginNode()
node_path = self.parseDumpProperty("Node-path", dump_props)
if self.matchDumpProperty("Node-kind"):
node_kind = self.parseDumpProperty("Node-kind", dump_props)
else:
node_kind = None
node_action = self.parseDumpProperty("Node-action", dump_props)
# A number of optional properties follow. We know what they
# can be, but their order isn't fixed.
#
# Content-length is optional, contrary to the available
# documentation, which claims that it is always present for
# compatability with generic rfc822 parsers.
#
# e.g. a dir node with action add and no properties has no
# lengths at all.
tlen, plen, clen = None, None, None
while self.matchDumpProperty():
name, value = self.parseDumpProperty(store=dump_props)
if name == "Text-content-length":
tlen = int(value)
elif name == "Prop-content-length":
plen = int(value)
elif name == "Content-length":
clen = int(value)
prop_delta = dump_props.get("Prop-delta") == "true"
if prop_delta:
assert self.version > 2, msg("""
Property deltas should not occur in this dumpfile.
Its format is too old to support them.
""")
text_delta = dump_props.get("Text-delta") == "true"
if text_delta:
assert self.version > 2, msg("""
Text deltas should not occur in this dumpfile.
Its format is too old to support them.
""")
if clen == None:
clen = 0
if plen == None:
plen = 0
if tlen != None:
assert tlen == clen - plen, msg("""
Content-Length must be the sum of Text-Content-Length and
Prop-Content-Length. This is not what was found:
Content-Length: %(clen)d
Text-Content-Length: %(tlen)d
Prop-Content-Length: %(plen)d
""" % locals())
else:
tlen = clen - plen
yield dump_props
if plen > 0 or tlen > 0:
yield self.parseBlankLine()
if plen > 0:
yield self.parseUserProperties(plen, prop_delta)
if tlen > 0:
text = self.getBytes(tlen)
assert len(text) == tlen, msg("""
Expected text to have length %d, instead it had length %d.
""" % (tlen, len(text)))
# We can only verify the checksum when text_deltas are not
# in use. When text_deltas are being used, the checksum
# refers to the *result* of applying the deltas and we
# have no idea how nor desire to do that here.
if not text_delta:
expected_chksum = dump_props.get("Text-content-md5")
if expected_chksum:
computed_chksum = md5(text).hexdigest()
assert expected_chksum == computed_chksum, msg("""
MD5 mismatch.
expected: %s,
computed: %s.
""" % (expected_chksum, computed_chksum))
yield TextContent(text)
# TextContent is always terminated by an 'extra' newline,
# which getBytes consumes for us, but does not return.
yield BlankLine()
for evt in self.parseBlankLines():
yield evt
yield EndNode()
def read(ses, fn, opt, progress=True):
# initial progress message
if progress:
ses.progress('reading %s' % fn)
# get concatenated list of chunks for all files
chunks = []
def get_chunks(fn):
if os.path.isdir(fn):
for f in sorted(os.listdir(fn)):
get_chunks(os.path.join(fn, f))
elif is_ftdc_file(fn):
chunks.extend(File.get(fn))
get_chunks(fn)
if not chunks:
raise Exception(fn + ' is not an ftdc file or directory')
# compute time ranges for each chunk using _id timestamp
for i in range(len(chunks)):
t = chunks[i]._id
fudge = -300 # xxx _id is end instead of start; remove when SERVER-20582 is fixed
chunks[i].start_time = t + fudge
if i > 0:
chunks[i - 1].end_time = t
chunks[-1].end_time = float(
'inf') # don't know end time; will filter last chunk later
# roughly filter by timespan using _id timestamp as extracted above
# fine filtering will be done during processing
in_range = lambda chunk: chunk.start_time <= opt.before and chunk.end_time >= opt.after
filtered_chunks = [chunk for chunk in chunks if in_range(chunk)]
# init stats for progress report
total_bytes = sum(len(chunk) for chunk in filtered_chunks)
read_chunks = 0
read_samples = 0
read_bytes = 0
used_samples = 0
# compute number of output samples desired for overview mode
# uses time-filtered data sizes so resolution automatically increases for smaller timespans
# returns a subset of the samples, aiming for each sample to represent same number of bytes,
# except that we return at least one sample for each chunk
if opt.overview == 'heuristic':
overview = 1000
util.msg('limiting output to %d samples; use --overview to override' %
overview)
elif opt.overview == 'none' or opt.overview == 'all' or not opt.overview:
overview = float('inf')
else:
overview = int(opt.overview)
overview_bytes = int(max(total_bytes / overview, 1))
# propagate sample numbers if we can
sample_number = 0 if filtered_chunks and chunks and filtered_chunks[
0] == chunks[0] else None
# we already filtered filtered_chunk_docs by type and time range
for chunk in filtered_chunks:
# propagate sample numbers if we can
if sample_number != None:
chunk.sample_number = sample_number
# compute desired subset of metrics based on target number of samples
max_samples = (read_bytes + len(chunk)
) / overview_bytes - read_bytes / overview_bytes
if max_samples <= 1:
metrics = chunk.get_first()
metrics = util.BSON((n, [v[0]]) for (n, v) in metrics.items())
used_samples += 1
else:
metrics = chunk.get_all()
every = int(math.ceil(float(chunk.nsamples) / max_samples))
if every != 1:
metrics = util.BSON(
(n, v[0::every]) for (n, v) in metrics.items())
used_samples += chunk.nsamples / every
yield metrics
# propagate sample numbers if we can
sample_number = chunk.sample_number + chunk.nsamples if chunk.sample_number != None else None
# report progress
read_chunks += 1
read_bytes += len(chunk)
read_samples += chunk.nsamples
if progress and (read_chunks % 10 == 0 or read_bytes == total_bytes):
msg = '%d chunks, %d samples, %d bytes (%.0f%%), %d bytes/sample; %d samples used' % (
read_chunks, read_samples, read_bytes, 100.0 * read_bytes /
total_bytes, read_bytes / read_samples, used_samples)
ses.progress(msg)
if used_samples != read_samples:
s = 'displaying overview of ~%d of ~%d samples in selected time range (use z to zoom in or v to view all)'
ses.advise(s % (used_samples, read_samples))
else:
ses.advise('displaying all ~%d samples in selected time range' %
used_samples)
def get_series(ses, spec, spec_ord):
# parse helper
def split(s, expect, err, full):
m = re.split('([' + expect + err + '])', s, 1)
s1, d, s2 = m if len(m)==3 else (m[0], '$', '')
if d in err:
msg = 'expected %s at pos %d in %s, found %s' % (expect, len(full)-len(s)+1, full, d)
raise Exception(msg)
return s1, d, s2
# parse the spec
left, d, s = split(spec, '(:=', ')', spec)
if d=='=': # has tag
tag = left
spec_name, d, s = split(s, '(:', ')=', spec)
else: # no tag
tag = None
spec_name = left
params = {}
if d == '(': # has args
while d != ')': # consume args
name, d, s = split(s, '=)', '(', spec) # get arg name
value, d, s = split(s, '(),', '', spec) # bare value
p = 0
while d=='(' or p>0: # plus balanced parens
value += d
if d=='(': p += 1
elif d==')': p -= 1
v, d, s = split(s, '(),', '', spec)
value += v
params[name] = value
fn = s.lstrip(':') # xxx canonicalize fn
util.dbg(spec_name, params, fn)
ses.add_title(fn)
def detect_file_type(fn):
if ftdc.is_ftdc_file_or_dir(fn):
return 'ftdc'
with open(fn) as f:
for _ in range(10):
try:
json.loads(f.next())
return 'json'
except Exception as e:
util.dbg(e)
return 'text'
file_type = detect_file_type(fn)
util.msg('detected type of', fn, 'as', file_type)
# find matching descriptors
scored = collections.defaultdict(list)
spec_name_words = util.words(spec_name)
for desc in descriptors.descriptors:
if get(desc,'file_type') != file_type:
continue
desc_name_words = util.words(desc['name'])
last_i = -1
beginning = matched = in_order = adjacent = 0
for w, word in enumerate(spec_name_words):
try:
i = desc_name_words.index(word)
if i==0 and w==0: beginning = 1
matched += 1
if i==last_i+1: adjacent += 1
elif i>last_i: in_order += 1
last_i = i
except ValueError:
pass
score = (beginning, matched, adjacent, in_order)
scored[score].append(desc)
best_score = sorted(scored.keys())[-1]
best_descs = scored[best_score] if best_score != (0,0,0,0) else []
series = [Series(spec, desc, params, fn, spec_ord, tag, ses.opt) for desc in best_descs]
# no match?
if not series:
util.msg('no descriptors match', spec_name)
return series
def main():
# Initialize new external memory dictionary.
util.msg('Populating external memory dictionary')
t1 = time.time()
dirname = util.make_temp_name('em_dict')
em_dict = pyrsistence.EMDict(dirname)
for i in util.xrange(random.randrange(0x1000)):
k = random.randrange(0x100000)
v = random.randrange(0x100000)
em_dict[k] = v
t2 = time.time()
util.msg('Done in %d sec.' % (t2 - t1))
# Request several iterator objects to locate possible memory leaks.
util.msg('Testing item iterator')
for i in util.xrange(0x1000):
for item in em_dict.items():
pass
util.msg('Testing keys iterator')
for i in util.xrange(0x1000):
for key in em_dict.keys():
pass
util.msg('Testing values iterator')
for i in util.xrange(0x1000):
for value in em_dict.values():
pass
t3 = time.time()
util.msg('Done in %d sec.' % (t3 - t2))
# Close and remove external memory dictionary from disk.
em_dict.close()
shutil.rmtree(dirname)
return 0
def parse(self, fileLike):
"""
Generate parse events from the bytes provided by fileLike.
"""
try:
self.reader = None
self.reader = Reader(fileLike)
self.reader.next()
for evt in self.parseDumpfile():
yield evt
except AssertionError, e :
sys.stderr.write(str(self.reader)+"\n")
raise
else:
assert self.reader.eof, msg("Stopped parsing before end of input\n"
+ str(self.reader))
def parseDumpfile(self):
"""
A Dumpfile consists of a Version, an (optional?) UUID, and
zero or more Revisions. Extra blank lines may occur. Blank
lines before and after the version declaration are not
reported.
"""
self.version = None
self.skipBlankLines()
version = int(self.parseDumpProperty("SVN-fs-dump-format-version"))
assert 2 <= version <= 3, \
"Only dump format versions 2 and 3 are supported"
self.version = version
self.skipBlankLines()
def main():
# Initialize new external memory dictionary.
util.msg('Populating external memory dictionary')
t1 = time.time()
dirname = util.make_temp_name('em_dict')
em_dict = pyrsistence.EMDict(dirname)
for i in util.xrange(random.randrange(0x1000)):
k = random.randrange(0x100000)
v = random.randrange(0x100000)
em_dict[k] = v
t2 = time.time()
util.msg('Done in %d sec.' % (t2 - t1))
# Request several iterator objects to locate possible memory leaks.
util.msg('Testing item iterator')
for i in util.xrange(0x1000):
for item in em_dict.items():
pass
util.msg('Testing keys iterator')
for i in util.xrange(0x1000):
for key in em_dict.keys():
pass
util.msg('Testing values iterator')
for i in util.xrange(0x1000):
for value in em_dict.values():
pass
t3 = time.time()
util.msg('Done in %d sec.' % (t3 - t2))
# Close and remove external memory dictionary from disk.
em_dict.close()
shutil.rmtree(dirname)
return 0
def data_point_after_splits(self, t, d, get_field, set_field):
# may not have data in case of a count, so just use 0
try:
d = float(d)
except:
d = 0
# wrapping 32-bit counter hack
if self.wrap:
if self.last_d > self.wrap/2 and d < -self.wrap/2:
self.wrap_offset += 2 * self.wrap
util.dbg('wrap', d, self.last_d, self.wrap_offset)
elif self.last_d < -self.wrap/2 and d > self.wrap/2:
self.wrap_offset -= 2 * self.wrap
util.dbg('wrap', d, self.last_d, self.wrap_offset)
self.last_d = d
d += self.wrap_offset
# compute a rate
if self.rate:
if self.last_t==t:
return
if self.last_t:
dd = d - self.last_d
if self.rate != 'delta':
dd /= t - self.last_t
self.last_t = t
self.last_d = d
d = dd
else:
self.last_t = t
self.last_d = d
return
if d < 0:
self.wrapped = True
if not self.rate:
util.msg('possible wrap detected in', self.get('name'), 'at', util.f2s(t))
# scale - xxx need general computation mechanism here instead
if self.scale_field:
scale_field = self.scale_field.format(**self.descriptor)
try:
div = float(get_field(scale_field))
except:
return
if div:
d /= div
d /= self.scale
# record the data
if self.buckets:
s0 = t
s1 = s0 // self.buckets * self.buckets
t = s1
self.ys[t] = self.op(self.ys, t, d)
elif self.queue:
if d>self.queue_min_ms:
ms = datetime.timedelta(0, d/1000.0)
self.queue_times.append((t-ms,+1))
self.queue_times.append((t,-1))
else:
self.ys[t] = d
# make data available for computation
if self.set_field and set_field:
set_field(self.set_field, d)
# tell our caller what we recorded
return d
def progress(self, msg):
if self.server:
self.put(msg + '<br/><script>this.document.body.scrollIntoView(false)</script>')
util.msg(msg)
def page(ses):
opt = ses.opt
# support for save in server mode
if ses.server:
ses.start_save()
# in server mode graphs were alread generated in the "progress" phase
if not ses.server:
_get_graphs(ses)
# start page
_head(ses)
ses.eltend('script', {}, 'document.title="%s"' % ', '.join(ses.title))
ses.elt('body', {
'onkeypress': 'key()',
'onload': 'loaded_content()',
#'onunload': "do_unload('body')",
})
# no data - finish with empty page and return
if not ses.graphs:
ses.put('NO DATA')
ses.endall()
return
# compute stats
spec_matches = collections.defaultdict(int)
for graph in ses.graphs:
for series in graph:
spec_matches[series.spec] += 1
spec_empty = collections.defaultdict(int)
spec_zero = collections.defaultdict(int)
# provide browser with required client-side parameters
if not hasattr(opt, 'cursors'): opt.cursors = []
model_items = [
'tleft', 'tright', 'cursors', 'level', 'before', 'after', 'live', 'selected', 'scrollY',
]
model = dict((n, getattr(opt, n)) for n in model_items if hasattr(opt, n))
spec_cmdline = ' '.join(pipes.quote(s) for s in opt.specs)
model['spec_cmdline'] = spec_cmdline
ses.advise('viewing ' + spec_cmdline + ' (use o or O to change)')
#util.msg(model)
ses.eltend('script', {}, 'top.model = %s' % json.dumps(model))
# state-dependent informational message
ses.advise('current detail level is <span id="current_level"></span> (hit 1-9 to change)', 0)
# help message at the top
ses.elt('div', {'onclick':'toggle_help()'})
ses.put('<b>click here for help</b></br>')
ses.elt('div', {'id':'help', 'style':'display:none'})
ses.put(help_all)
if ses.server:
ses.put(help_server)
ses.put('<br/>')
ses.end('div')
ses.end('div')
ses.put('<br/>'.join(ses.advice))
ses.put('<br/><br/>')
# table of graphs
ses.elt('table', {'id':'table', 'style':'position:relative;'})
# this row holds cursor heads, cursor letters, and time labels
ses.elt('tr')
ses.eltend('td')
ses.eltend('td')
ses.elt('td')
cursors_html(ses, opt.width, opt.tmin, opt.tmax, opt.ticks)
ses.end('td')
ses.end('tr')
# this row holds data column heads (min, max, name)
ses.elt('tr')
ses.td('head data', 'avg')
ses.td('head data', 'max')
ses.eltend('td')
if opt.number_rows:
ses.td('head row-number', 'row')
ses.td('head desc', 'name')
ses.td('', ' ')
ses.end('tr')
# function to emit a graph
def emit_graph(data, ymax=None, sparse=False):
graphing.html_graph(
ses, data=data,
tmin=opt.tmin, tmax=opt.tmax, width=opt.width,
ymin=0, ymax=ymax, height=opt.height,
#ticks=ticks, shaded=not opt.no_shade and len(data)==1)
ticks=opt.ticks, shaded=len(data)==1, bins=opt.bins,
sparse=sparse
)
# colors for merged graphs
colors = ['rgb(50,102,204)','rgb(220,57,24)','rgb(253,153,39)','rgb(20,150,24)',
'rgb(153,20,153)', 'rgb(200,200,200)']
def color(i):
return colors[i] if i <len(colors) else 'black'
# word-by-word common prefix
# used to factor out common prefix and suffix in merged graph names
def commonprefix(names):
pfx = []
for words in zip(*[n.split() for n in names]):
if all(w==words[0] for w in words):
pfx.append(words[0])
else:
break
return ' '.join(pfx)
# format graph name, factoring out common prefixes and common suffixes for merged graphs
def name_td(g):
ses.td('name')
pfx = commonprefix([s.name for s in g])
sfx = commonprefix([s.name[::-1] for s in g])[::-1]
ses.put(pfx)
if sfx != pfx:
for i,s in enumerate(g):
mid = ' ' + s.name[len(pfx):len(s.name)-len(sfx)]
ses.eltend('span', {'style':'color:%s' % color(i)}, mid)
ses.put(sfx)
ses.end('td')
# determine which graphs to show, suppressing empty and uniformly zero if desired
# emit placeholders (graph==None, generating empty tr) to facilitate maintaining order
rows = []
for graph in sorted(ses.graphs, key=lambda g: g[0].sort_ord):
graph.sort(key=lambda s: s.sort_ord)
graph.ymin = min(s.ymin for s in graph)
graph.ymax = max(s.ymax for s in graph)
graph.ysum = sum(s.ysum for s in graph)
graph.wrapped = any(s.wrapped for s in graph)
graph.ylen = sum(len(s.ys) for s in graph)
graph.display_ymax = max(s.display_ymax for s in graph)
if graph.ylen:
if graph.ymax!=0 or graph.ymin!=0 or opt.show_zero:
rows.append(graph)
else:
rows.append(None) # placeholder
util.dbg('skipping uniformly zero data for', graph[0].get('name'), 'in', graph[0].fn)
for s in graph:
spec_zero[s.spec] += 1
elif opt.show_empty:
rows.append(graph)
else:
rows.append(None) # placeholder
util.dbg('no data for', graph[0].get('name'), 'in', graph[0].fn)
for s in graph:
spec_empty[s.spec] += 1
# emit html for graphs we are showing, in the requested order
if hasattr(opt,'row_order') and len(opt.row_order)==len(rows):
row_order = opt.row_order
else:
row_order = range(len(rows))
for row in row_order:
graph = rows[row]
if graph==None: # placeholder
ses.eltend('tr', {
'class': 'row',
'_level': 1000,
'_row': row,
})
elif graph.ylen:
ses.elt('tr', {
'onclick': 'sel(this)',
'class': 'row',
'_level': graph[0].level,
'_row': row,
})
avg = '{:,.3f}'.format(float(graph.ysum)/graph.ylen) if not graph.wrapped else 'WRAPPED'
ses.td('data', avg)
ses.td('data', '{:,.3f}'.format(graph.ymax))
ses.td('graph')
graph_color = lambda graph, i: color(i) if len(graph)>1 else 'black'
data = [(s.ts, s.ys, graph_color(graph,i)) for i,s in enumerate(graph)]
emit_graph(data, graph.display_ymax, graph.sparse)
ses.end('td')
if opt.number_rows:
ses.td('row-number', str(row))
row += 1
name_td(graph)
ses.end('tr')
else:
ses.elt('tr', {'onclick':'sel(this)', 'class':'row', '_level':graph[0].level})
ses.td('data', 'n/a')
ses.td('data', 'n/a')
ses.td('graph')
emit_graph([])
ses.end('td')
if opt.number_rows:
ses.td('row-number', str(row))
name_td(graph)
ses.end('tr')
# close it out
ses.endall()
for spec in opt.specs:
util.msg('spec', repr(spec), 'matched:', spec_matches[spec],
'zero:', spec_zero[spec], 'empty:', spec_empty[spec])
threading.Thread.__init__(self)
def run(self):
while 1:
if task_queue.empty() == True:
break
task = task_queue.get()
module[task['module']].exploit(task['request'])
if __name__ == '__main__':
O = {}
NODE_KEY = "a88b92531ba974f68bc1fd5938fc77"
NODE_DEBUG = 0
SERVER = "http://w/uauc/playweb/"
util.msg("PlayWeb Node 1.0")
util.msg("Server:%s Key:%s Debug:%d" % (SERVER, NODE_KEY, NODE_DEBUG))
util.msg("Listening server project...")
while 1:
r = util.http_get(SERVER + "/index.php?m=node&a=get_task")
if r['data'] != " " :
O = eval(util.decode_str(r['data'], NODE_KEY))
break
time.sleep(1)
O['debug'] = NODE_DEBUG
util.msg("[Project] Target:%s Time:%s Module:%s Thread:%s" % (O['target'], util.date(O['start_time']), O['module'], O['thread']), 1)
O['target'] = "w"
O['key'] = NODE_KEY
#O['depth'] = 5 # notice
O['server_url'] = SERVER + "?m=node&a="
O['web-ports'] = util.csv2array(O['web-ports'])
import util
import DB
import sqlite3
import sys
# global
space = 50
# test of data base connection
util.welcome_msg(space)
try:
DB.init_db()
util.msg('This is your firse time log in', space)
util.msg('Wish you happy with my service', space)
except:
util.log('DB ok')
while (1):
cmd = input('<< ')
if (cmd == 'e'): sys.exit()
elif (cmd == 'h'): util.info(space)
elif (cmd == 'n'): DB.insert(space)
elif (cmd == 'l'): DB.list_account(space)
elif (cmd == 't'): DB.list_tag(space)
elif (cmd == 'u'): DB.update(space)
elif (cmd == 'd'): DB.delete(space)
else:
util.welcome_msg(space)
def read(ses, fn, opt, progress=True):
# initial progress message
if progress:
ses.progress('reading %s' % fn)
# get concatenated list of chunks for all files
chunks = []
def get_chunks(fn):
if os.path.isdir(fn):
for f in sorted(os.listdir(fn)):
get_chunks(os.path.join(fn,f))
elif is_ftdc_file(fn):
chunks.extend(File.get(fn))
get_chunks(fn)
if not chunks:
raise Exception(fn + ' is not an ftdc file or directory')
# compute time ranges for each chunk using _id timestamp
for i in range(len(chunks)):
t = chunks[i]._id
fudge = -300 # xxx _id is end instead of start; remove when SERVER-20582 is fixed
chunks[i].start_time = t + fudge
if i>0:
chunks[i-1].end_time = t
chunks[-1].end_time = float('inf') # don't know end time; will filter last chunk later
# roughly filter by timespan using _id timestamp as extracted above
# fine filtering will be done during processing
in_range = lambda chunk: chunk.start_time <= opt.before and chunk.end_time >= opt.after
filtered_chunks = [chunk for chunk in chunks if in_range(chunk)]
# init stats for progress report
total_bytes = sum(len(chunk) for chunk in filtered_chunks)
read_chunks = 0
read_samples = 0
read_bytes = 0
used_samples = 0
# compute number of output samples desired for overview mode
# uses time-filtered data sizes so resolution automatically increases for smaller timespans
# returns a subset of the samples, aiming for each sample to represent same number of bytes,
# except that we return at least one sample for each chunk
if opt.overview=='heuristic':
overview = 1000
util.msg('limiting output to %d samples; use --overview to override' % overview)
elif opt.overview=='none' or opt.overview=='all' or not opt.overview:
overview = float('inf')
else:
overview = int(opt.overview)
overview_bytes = int(max(total_bytes / overview, 1))
# propagate sample numbers if we can
sample_number = 0 if filtered_chunks and chunks and filtered_chunks[0]==chunks[0] else None
# we already filtered filtered_chunk_docs by type and time range
for chunk in filtered_chunks:
# propagate sample numbers if we can
if sample_number != None:
chunk.sample_number = sample_number
# compute desired subset of metrics based on target number of samples
max_samples = (read_bytes+len(chunk)) / overview_bytes - read_bytes / overview_bytes
if max_samples <= 1:
metrics = chunk.get_first()
metrics = util.BSON((n,[v[0]]) for (n,v) in metrics.items())
used_samples += 1
else:
metrics = chunk.get_all()
every = int(math.ceil(float(chunk.nsamples)/max_samples))
if every != 1:
metrics = util.BSON((n,v[0::every]) for (n,v) in metrics.items())
used_samples += chunk.nsamples / every
yield metrics
# propagate sample numbers if we can
sample_number = chunk.sample_number+chunk.nsamples if chunk.sample_number!=None else None
# report progress
read_chunks += 1
read_bytes += len(chunk)
read_samples += chunk.nsamples
if progress and (read_chunks%10==0 or read_bytes==total_bytes):
msg = '%d chunks, %d samples, %d bytes (%.0f%%), %d bytes/sample; %d samples used' % (
read_chunks, read_samples, read_bytes, 100.0*read_bytes/total_bytes,
read_bytes/read_samples, used_samples
)
ses.progress(msg)
if used_samples != read_samples:
s = 'displaying overview of ~%d of ~%d samples in selected time range (use z to zoom in or v to view all)'
ses.advise(s % (used_samples, read_samples))
else:
ses.advise('displaying all ~%d samples in selected time range' % used_samples)
def process(series, fn, opt):
# to track metrics present in the data but not processed by any series
unrecognized = set()
# xxx does time parsing belong here or in the parse routines?
pt = util.parse_time()
# process all chunk that we are sent
while True:
try:
# get our next input
chunk = yield
def process_series(s, data_key):
tz = chunk.tz if hasattr(chunk, 'tz') else s.tz
time_key = s.time_key # e.g. 'serverStatus.localTime'
if data_key in chunk and time_key in chunk:
ts = chunk[time_key]
if type(ts[0]) == str or type(ts[0]) == unicode:
for i, t in enumerate(ts):
ts[i] = pt.parse_time(t, opt, tz)
if ts[0] / s.time_scale > opt.before or ts[
-1] / s.time_scale < opt.after:
return
for i, (t, d) in enumerate(zip(ts, chunk[data_key])):
t = t / s.time_scale
if t >= opt.after and t <= opt.before:
def get_field(key):
try:
return chunk[key][i]
except IndexError:
return None
if d != None:
s.data_point(t, d, get_field, None, opt)
# send each series our data points
for s in series:
if s.special:
s.special(chunk)
if s.split_on_key_match:
for data_key in chunk:
if data_key == s.time_key:
continue
m = s.split_on_key_match_re.match(data_key)
if m:
description = m.groupdict()
ss = s.get_split(data_key, description)
process_series(ss, data_key)
else:
process_series(s, s.data_key)
# track what we have used
unrecognized.update(chunk.keys())
except GeneratorExit:
break
except Exception as e:
traceback.print_exc()
raise Exception('error while processing ' + fn + ': ' + str(e))
# compute and print unrecognized metrics
ignore = re.compile('^serverStatus.(repl|start|end)|'
'^replSetGetStatus|slot_closure_rate')
for s in series:
unrecognized.discard(s.data_key)
unrecognized.discard(s.time_key)
unrecognized = filter(lambda x: not ignore.match(str(x)), unrecognized)
is_str = lambda x: type(x) == str or type(x) == unicode
unrecognized = filter(lambda x: x in chunk and not is_str(chunk[x][0]),
unrecognized)
if unrecognized:
util.msg('unrecognized metrics:')
for u in sorted(unrecognized):
util.msg(' ', u)
def do_GET(self):
# parse command-line args passed in url query string as an 'args' parameter
def query2opt(query):
args = shlex.split(query['args'][0])
return __main__.get_opt(args)
# parse url, extracting path and query portions
_, _, path, _, query, _ = urlparse.urlparse(self.path)
query = urlparse.parse_qs(query)
# query to root is redirected to default session 0
if path == '/':
self.send_response(301) # permanent
self.send_header('Location', '/0')
# open a new view in a new window
# expects command-line arg string in url parameter "args"
# parse off the query, open new session based on that, then redirect to bare session url
elif path == '/open':
opt = query2opt(query) # parse url "args" parameter
ses = Ses(opt, server=True) # new session
self.send_response(302) # temporary redirect
self.send_header('Location', ses.path)
# top-level page: return the container, which includes
# progress message area - loaded via /ses/progress url in progress phase (below)
# content area - loaded via /ses/content url in content phase (below)
elif path in Ses.sessions:
ses = Ses.sessions[path]
self.prepare(ses)
html.container(ses)
# info for a given time t
elif path.endswith('/info'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
t = float(query['t'][0])
self.prepare(ses)
html.info(ses, t)
# raw info for a given time t
elif path.endswith('/raw'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
t = float(query['t'][0])
self.prepare(ses)
html.raw(ses, t, kind='raw')
elif path.endswith('/metadata'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
t = float(query['t'][0])
self.prepare(ses)
html.raw(ses, t, kind='metadata')
# progress phase: load the data in preparation for generating content
# while emitting progress messages. We also accept new view parameters to open
# new view in current window as command-line arg string in url parameter "args"
elif path.endswith('/progress'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
if 'args' in query:
ses.opt = query2opt(query) # parse url "args" parameter
self.prepare(ses)
html.load(ses)
# content phase: generate actual html view from graph data loadedin progress phase
elif path.endswith('/content'):
path = path.rsplit('/', 1)[0]
ses = Ses.sessions[path]
self.prepare(ses)
html.page(ses)
# a window closed
elif '/close/' in path:
if Handler.exit_on_close:
path, _, what = path.rsplit('/', 2)
util.msg('closing', path, '(' + what + ')')
if path in Ses.sessions:
del Ses.sessions[path]
if not Ses.sessions:
util.msg('all sessions closed, exiting')
os._exit(0)
# otherwise not found
else:
self.send_response(404) # not found
def browser(opt, url):
# what os?
if sys.platform == 'darwin':
cmd = 'sleep 1; open -a "Google Chrome" "%s"' % url
elif sys.platform == 'linux2':
cmd = 'sleep 1; google-chrome "%s" &' % url
elif sys.platform == 'win32':
cmd = 'timeout 2 && start /b chrome "%s" &' % url
else:
raise Exception('unknown platform ' + sys.platform)
# launch it
if cmd:
util.msg('opening a browser window on', url)
rc = subprocess.call(cmd, shell=True)
if rc != 0:
util.msg('can\'t open browser; is Google Chrome installed?')
else:
util.msg('don\'t know how to open a browser on your platform')
# go into background
# not as robust as daemonizing, but that's not needed, and adds an external dependency
if not opt.nofork:
log_fn = 'timeseries.%d.log' % opt.port
util.msg('going into background; sending output to ' + log_fn)
util.msg('will terminate when browser window closes')
util.msg('use --nofork to run in foreground')
if os.fork():
os._exit(0)
sys.stdin.close()
sys.stderr = sys.stdout = open(log_fn, 'a')
util.msg('\n===', url)
signal.signal(signal.SIGHUP, signal.SIG_IGN)
def parseUserPropertyEnd(self):
assert self.matchUserPropertyEnd(), msg("""
Expected PROPS-END, but found\n%s
""" % (self.reader,))
self.reader.next()
import jsonEncoder
import networkUtil # Custom Network functions (WIFI + MQTT)
from umqtt.simple import MQTTClient
# Entry Point Indication
util.dots()
# Setup led
green = led.Led(13)
red = led.Led(15)
# Setup i2c Bus
i2c = machine.I2C(-1, machine.Pin(5), machine.Pin(4))
util.msg('i2c bus created')
# Instantiate Temperature sensor
#Address of TMP007 Temperature Sensor
temp007Address = 64
tempSensor = temp007.Temp007(i2c, temp007Address)
util.msg('Temp007 instantiated, name: tempSensor')
# Instantiate Proximity sensor
#Address of VCNL4010 Proximity Sensor
proxAddress = 19
proxSensor = vcnl4010.Vcnl4010(i2c, proxAddress)
proxSensor.setup()
util.msg('Vcnl instantiated, name: proxSensor')
# Instantiate 2 servos
