def assertIO(self, input, output):
stdout, stdin = sys.stdout, sys.stdin
sys.stdout, sys.stdin = StringIO(), StringIO(input)
resolve()
sys.stdout.seek(0)
out = sys.stdout.read()[:-1]
sys.stdout, sys.stdin = stdout, stdin
self.assertEqual(out, output)
def main():
if "M" in options.debug:
import pdb
pdb.set_trace()
if not options.filelist:
options.parser.print_help()
return
if options.output == "-":
fp = sys.stdout
elif options.output:
fp = open(options.output, "w")
else:
fp = None
if fp:
print_header(fp)
nerrors = 0
for i, options.filename in enumerate(options.filelist):
try:
if options.verbose:
print(i, options.filename)
if not options.filename.endswith(".m"):
print("\tIgnored: '%s' (unexpected file type)" %
options.filename)
continue
if basename(options.filename) in options.xfiles:
if options.verbose:
print("\tExcluded: '%s'" % options.filename)
continue
buf = open(options.filename).read()
buf = buf.replace("\r\n", "\n")
# FIXME buf = buf.decode("ascii", errors="ignore")
stmt_list = parse.parse(buf if buf[-1] == '\n' else buf + '\n')
if not stmt_list:
continue
if not options.no_resolve:
G = resolve.resolve(stmt_list)
if not options.no_backend:
s = backend.backend(stmt_list)
if not options.output:
f = splitext(basename(options.filename))[0] + ".py"
with open(f, "w") as fp:
print_header(fp)
fp.write(s)
else:
fp.write(s)
#fp.close()
except KeyboardInterrupt:
break
except:
nerrors += 1
traceback.print_exc(file=sys.stdout)
if options.strict:
break
finally:
pass
if nerrors:
print("Errors:", nerrors)
def sed(request):
context = {'sr': 1/3600, 'log': []}
if request.method == 'POST':
# Form submission handling
coords = request.POST.get('coords')
sr = 1/3600
name,ra,dec = resolve(coords)
for _ in ['coords', 'preview']:
context[_] = request.POST.get(_)
if not name:
context['message'] = "Can't resolve position: " + coords
else:
context['name'] = name
context['ra'] = ra
context['dec'] = dec
context['sr'] = sr
work = sed_worker(ra, dec, sr)
context['cats'] = work['cats']
context['log'] = work['log']
return TemplateResponse(request, 'sed.html', context=context)
def compile(self, rdql):
from lex import Lexer
from yacc import Parser
self.ast = Parser().parse(rdql, lexer=Lexer())
self.ast = resolve(self.ast)
select, count, self.ast = generate(self.ast)
return select, count
def Init(parameters):
Log.node_name = parameters['NODENAME']
Log.address = (resolve(parameters['LOGGER'])[0], 8083)
#
# Open the socket to the logging endpoint
#
Log.socket = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
def callgraph(func_list):
"""
Build callgraph of func_list, ignoring
built-in functions
"""
G = nx.DiGraph()
for func in func_list:
G.add_node(func.head.ident.name)
for func in func_list:
assert isinstance(func,node.function)
func_name = func.head.ident.name
resolve.resolve(func)
for s in node.postorder(func):
if (s.__class__ is node.funcall and
s.func_expr.__class__ is node.ident and
s.func_expr.name in G.nodes()):
G.add_edge(func_name,s.func_expr.name)
return G
def callgraph(func_list):
"""
Build callgraph of func_list, ignoring
built-in functions
"""
G = nx.DiGraph()
for func in func_list:
G.add_node(func.head.ident.name)
for func in func_list:
assert isinstance(func, node.function)
func_name = func.head.ident.name
resolve.resolve(func)
for s in node.postorder(func):
if (s.__class__ is node.funcall
and s.func_expr.__class__ is node.ident
and s.func_expr.name in G.nodes()):
G.add_edge(func_name, s.func_expr.name)
return G
def main():
tar = None
if not options.filelist:
options.parser.print_help()
return
if (len(options.filelist) == 1 and options.filelist[0].endswith(".tar")):
tar = tarfile.open(options.filelist[0])
options.filelist = tar.getnames()
if options.output == "-":
fp = sys.stdout
elif options.output:
fp = open(options.output, "w")
else:
assert not options.output
filename, filetype = splitext(basename(options.filelist[0]))
options.output = filename + ".py"
fp = open(options.output, "w")
print >> fp, "# Autogenerated with SMOP " + version.__version__
#print >> fp, "from __future__ import division"
print >> fp, "from smop.core import *"
if options.link:
print >> fp, "from %s import *" % options.link
print >> fp, "#", options.filename
for i, options.filename in enumerate(options.filelist):
try:
if not options.filename.endswith((".m")):
if options.verbose:
print "\tIgnored: '%s' (unexpected file type)" % options.filename
continue
if os.path.basename(options.filename) in options.xfiles:
print "\tExcluded: '%s'" % options.filename
continue
if options.verbose:
print options.filename
if tar:
buf = tar.extractfile(options.filename).read()
else:
buf = open(options.filename).read()
buf = buf.replace("\r\n", "\n")
buf = buf.decode("ascii", errors="ignore")
stmt_list = parse.parse(buf if buf[-1] == '\n' else buf + '\n')
#assert None not in stmt_list
if not stmt_list:
return
if not options.no_resolve:
G = resolve.resolve(stmt_list)
if not options.no_backend:
s = backend.backend(stmt_list)
print >> fp, s
except Exception as e:
print "\tFailed: ", options.filename
if not options.ignore:
raise
options.ignore -= 1
def main():
if len(sys.argv) != 2:
print("Usage: " + os.path.basename(__file__) + " path/to/library")
exit(1)
path = os.path.abspath(__file__)
os.chdir(os.path.dirname(path))
path_to_library = os.path.abspath(sys.argv[1])
resolved_content = resolve.resolve(path_to_library)
return_code = copy_to_clipboard(resolved_content)
exit(return_code)
def secondscale_map(request, ra=0, dec=0, sr=0.01, size=600):
if request.method == 'POST':
coords = request.POST.get('coords')
sr = float(request.POST.get('sr'))
name, ra, dec = resolve(coords)
return redirect('/secondscale/map/coords/%g/%g/%g' % (ra, dec, sr))
if ra and dec:
ra = float(ra)
dec = float(dec)
sr = float(sr) if sr else 0.01
records = Records.objects.extra(where=[
"q3c_radial_query(ra, dec, %s, %s, %s)"
],
params=(ra, dec, sr)).order_by('time')
x = []
y = []
mag = []
f = []
for r in records:
x.append(r.ra)
y.append(r.dec)
mag.append(r.mag)
f.append(favor2_filters.get(r.filter.id))
dpi = 72
figsize = (size / dpi, size / dpi)
fig = Figure(facecolor='white', figsize=figsize)
ax = fig.add_subplot(111)
formatter = ScalarFormatter(useOffset=False)
ax.xaxis.set_major_formatter(formatter)
ax.yaxis.set_major_formatter(formatter)
ax.scatter(x, y, c=f)
ax.set_xlabel("RA")
ax.set_ylabel("Dec")
ax.set_title("Map at (%g, %g), radius %g" % (ra, dec, sr))
# 10% margins on both axes
ax.margins(0.1, 0.1)
canvas = FigureCanvas(fig)
response = HttpResponse(content_type='image/png')
canvas.print_png(response)
return response
def secondscale_info(request, ra=0, dec=0, sr=0.01, size=1000):
if request.method == 'POST':
coords = request.POST.get('coords')
sr = request.POST.get('sr')
sr = float(sr) if sr else 0.01
name, ra, dec = resolve(coords)
return redirect('/secondscale/coords/%g/%g/%g' % (ra, dec, sr))
return TemplateResponse(request,
'secondscale_info.html',
context={
'ra': ra,
'dec': dec,
'sr': sr
})
def survey_info(request, ra=0, dec=0, sr=0.1, filter=True, imtype='survey'):
if request.method == 'POST':
coords = request.POST.get('coords')
sr = request.POST.get('sr')
sr = float(sr) if sr else 0.01
name, ra, dec = resolve(coords)
return redirect('/survey/%g/%g/%g' % (ra, dec, sr))
if request.GET.has_key('type'):
imtype = request.GET.get('type', 'survey')
context = {}
context['ra'] = ra
context['dec'] = dec
context['sr'] = sr
# TODO: expand the search area a bit and filter images containing the point
images = Images.objects.extra(
where=["q3c_radial_query(ra0, dec0, %s, %s, %s)"],
params=(ra, dec, 7.0),
select={
'filter_string': 'get_filter_name(filter)'
}).filter(type=imtype).order_by('-time')
if request.method == 'GET' and request.GET.get('channel_id'):
images = images.filter(channel_id=int(request.GET.get('channel_id')))
if request.method == 'GET':
filter = int(request.GET.get('filter', 1))
if filter and filter == 1:
images = [
i for i in images if check_pos(i.keywords, float(ra), float(dec))
]
if filter and filter == 2:
images = images.extra(where=[
"id IN (SELECT DISTINCT frame FROM records2 WHERE q3c_radial_query(ra, dec, %s, %s, %s))"
],
params=(ra, dec, 0.01))
context['images'] = images
return TemplateResponse(request, 'survey_info.html', context=context)
def lookup(nodes, interfaces):
# join nodes to interfaces
node_to_ips = {}
missing = []
for name, n in nodes.iteritems():
ips = []
for i in n['interface_ids']:
ip = interfaces[i]['ip']
if ip:
ips.append(ip)
if ips:
node_to_ips[name] = ips
else:
missing.append(name)
# if IP is not in PLCAPI, do the lookup ourselves
if len(missing) > 0:
node_to_ips.update(resolve.resolve(missing))
return node_to_ips
def __init__(self, node, state, src_port_index, dst_node, dst_port_index,
dst_uid):
dst_port = self.PORT_OFFSET + dst_port_index if state == 'Enabled' else self.PORT_DEAD
dst_addr, _ = resolve(dst_node)
src_addr, _ = node.env['profile']['address'].split(':')
self.node = node
self.state = state
self.index = src_port_index
self.remote_port = 0
self.remote_uid = 0
self.training_state = 0
self.lock = Lock()
self.remote_addr = (dst_addr, dst_port)
self.socket = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
self.address = socket.gethostbyname(src_addr)
self.socket.bind((self.address, src_port_index + self.PORT_OFFSET))
def uv_only(request, size=512):
context = {'sr': 0.1, 'log': []}
if request.method == 'POST':
# Form submission handling
coords = request.POST.get('coords')
sr = float(request.POST.get('sr', 0.1))
name,ra,dec = resolve(coords)
for _ in ['coords', 'preview', 'nuv', 'fuv']:
context[_] = request.POST.get(_)
if not name:
context['message'] = "Can't resolve position: " + coords
else:
context['name'] = name
context['ra'] = ra
context['dec'] = dec
context['sr'] = float(sr) if sr else 0.1
work = uv_only_worker(ra, dec, sr)
context['cats'] = work['cats']
if work['galex']:
table = work['galex']['table']
table = table[work['nidx']]
if request.POST.get('nuv'):
table = table[table['NUV'] < float(request.POST.get('nuv'))]
if request.POST.get('fuv'):
table = table[table['FUV'] < float(request.POST.get('fuv'))]
context['table'] = table
context['has_sdss'] = 'sdss' in [_['name'] for _ in work['cats']]
context['log'] = work['log']
return TemplateResponse(request, 'uv-only.html', context=context)
def survey_photometry(request, imtype='survey'):
context = {}
ra, dec, sr = None, None, 0.01
if request.method == 'POST':
coords = request.POST.get('coords')
sr = request.POST.get('sr')
sr = float(sr) if sr else 0.01
context['coords'] = coords
name, ra, dec = resolve(coords)
context['name'] = name
if request.POST.get('bv'):
context['bv'] = request.POST.get('bv')
if request.POST.get('vr'):
context['vr'] = request.POST.get('vr')
if request.POST.get('period'):
context['period'] = request.POST.get('period')
context['ra'] = ra
context['dec'] = dec
context['sr'] = sr
if ra is not None and dec is not None:
record = Records.objects.extra(
where=["q3c_radial_query(ra, dec, %s, %s, %s)"],
params=(ra, dec, sr)).filter(filter=0).order_by('quality').first()
if record:
context['best_image'] = record.frame.id
return TemplateResponse(request, 'survey_photometry.html', context=context)
try:
symtab = {}
for func_obj in func_list:
try:
func_name = func_obj.head.ident.name
symtab[func_name] = func_obj
print "\t",func_name
except AttributeError:
if verbose:
print "\tJunk ignored"
if strict:
return
continue
if options.do_resolve:
resolve.resolve(func_obj)
if options.do_typeof:
for func_obj in func_list:
t = func_obj.apply([],symtab)
if options.do_rewrite:
for func_obj in func_list:
rewrite.rewrite(func_obj)
for func_obj in func_list:
s = backend.backend(func_obj)
print >> fp, s
except Exception as ex:
print repr(ex)
if strict:
print "... t=123"
print "!exec foo(3)"
continue
if buf[0] == '!':
try:
exec buf[1:]
except:
print "eh?"
continue
t = parse.parse(buf if buf[-1] == '\n' else buf + '\n')
if not t:
continue
except EOFError:
return
resolve.resolve(t, symtab)
_ = backend.backend(t)
print _
if not output:
output = "a.py"
fp = open(output, "w") if output != "-" else sys.stdout
print >> fp, "# Autogenerated with SMOP version " + __version__
print >> fp, "# " + " ".join(sys.argv)
print >> fp, "from __future__ import division"
print >> fp, "from runtime import *"
for pattern in args:
for filename in glob.glob(os.path.expanduser(pattern)):
if not filename.endswith(".m"):
print "\tIngored file: '%s'" % filename
def Resolve(tree, GeneToSpecies):
StoreSpeciesSets(tree, GeneToSpecies)
for n in tree.traverse("postorder"):
tree = resolve.resolve(n, GeneToSpecies)
return tree
def secondscale_lightcurve(request,
ra=0,
dec=0,
sr=0.01,
size=1000,
type='mag'):
type = type or 'mag'
if request.method == 'POST':
coords = request.POST.get('coords')
sr = float(request.POST.get('sr'))
name, ra, dec = resolve(coords)
return redirect('/secondscale/lightcurve/coords/%g/%g/%g' %
(ra, dec, sr))
if ra and dec:
ra = float(ra)
dec = float(dec)
sr = float(sr) if sr else 0.01
records = Records.objects.extra(where=[
"q3c_radial_query(ra, dec, %s, %s, %s)"
],
params=(ra, dec, sr)).order_by('time')
x = []
y = []
y1 = []
y2 = []
f = []
for r in records:
x.append(r.time)
if type == 'mag':
y.append(r.mag)
y1.append(r.mag - r.mag_err)
y2.append(r.mag + r.mag_err)
else:
y.append(r.flux)
y1.append(r.flux - r.flux_err)
y2.append(r.flux + r.flux_err)
f.append(favor2_filters.get(r.filter.id))
dpi = 72
figsize = (size / dpi, 600 / dpi)
fig = Figure(facecolor='white', figsize=figsize)
ax = fig.add_subplot(111)
ax.autoscale()
#ax.plot(x, y, ".")
ax.scatter(x, y, c=f, marker='.', edgecolors=f)
ax.vlines(x, y1, y2, colors=f)
if records: # It is failing if no points are plotted
ax.xaxis.set_major_formatter(DateFormatter('%Y.%m.%d %H:%M:%S'))
ax.set_xlabel("Time, UT")
if type == 'mag':
ax.set_ylabel("Magnitude")
ax.invert_yaxis()
else:
ax.set_ylabel("Flux, ADU")
ax.set_title("Lightcurve at (%g, %g), radius %g" % (ra, dec, sr))
fig.autofmt_xdate()
# 10% margins on both axes
ax.margins(0.1, 0.1)
canvas = FigureCanvas(fig)
response = HttpResponse(content_type='image/png')
canvas.print_png(response)
return response
selecao += 9
elif key == 'a':
if (selecao - 1) >= 1:
selecao -= 1
elif key == 'd':
if (selecao + 1) <= 81:
selecao += 1
elif key in ['0','1','2','3','4','5','6','7','8','9','.']:
jogo = tratador(jogo,key, lg, lr, cg, cr)
elif key == 'n':
from novo_jogo import novo_jogo
jogo,solucao = novo_jogo(jogo,solucao)
elif key == 'z':
from salva_jogo import salva_jogo
salva_jogo(jogo, solucao)
elif key == 'f':
from fecha_jogo import fecha_jogo
resposta = fecha_jogo()
if resposta in ['s', 'S']:
break
elif key == 'x':
from resolve import resolve
jogo, solucao = resolve(jogo, solucao)
lg, lr, cg, cr = desenha_sudoku(window1, jogo, selecao)
key = window1.getch()
curses.endwin()
continue
print('Instrumentation finished')
print('Profiling: %s' % full_path)
output = None
lib = get_lib(full_path)
if not os.path.exists(d8_path):
print("Wrong d8_path. Set correct d8_path.")
exit()
cmd = [d8_path]
if len(lib) > 0:
cmd.append(lib)
cmd.append(ins_path)
output = None
try:
output = subprocess.check_output(cmd, timeout=30)
except subprocess.TimeoutExpired as e:
output = e.output
except subprocess.CalledProcessError as e:
output = e.output
print('Profiling finished')
records = resolve.resolve(output)
if len(records) > 0:
with open(type_path, 'wb') as f:
f.write(json.dumps(records).encode())
else:
print("Wrong corpus directory path")
FNULL.close()
def getDetails():
if request.method == "POST":
domain = request.form['domain']
s = resolve.resolve(domain)
# print(s)
return s
def pscheduler():
return resolve('pyramid_scheduler.pscheduler:main')()
def proxy(argv=sys.argv):
pcmd = argv[0][argv[0].rindex('i-') + 2:]
return resolve('pyramid.scripts.' + pcmd + ':main')(argv=argv)
def images_list(request,
night='',
type='all',
ra='',
dec='',
sr='5.0',
channel=0):
if request.method == 'POST':
coords = request.POST.get('coords')
sr = float(request.POST.get('sr'))
type = request.POST.get('type')
name, ra, dec = resolve(coords)
if not type or type == 'all':
return redirect('/images/coords/%g/%g/%g' % (ra, dec, sr))
else:
return redirect('/images/coords/%g/%g/%g/type/%s' %
(ra, dec, sr, type))
if ra and dec:
# Positional query
ra = float(ra)
dec = float(dec)
sr = float(sr) if sr else 5.0
images = Images.objects.extra(
select={
'filter_string': 'get_filter_name(filter)'
},
where=["q3c_radial_query(ra0, dec0, %s, %s, %s)"],
params=(ra, dec, sr)).order_by('-time')
#images = Images.objects.raw("SELECT *, get_filter_name(filter) AS filter_string FROM images WHERE q3c_radial_query(ra0, dec0, %s, %s, %s) ORDER BY time DESC", (ra, dec, sr))
query_type = 'positional'
elif night:
# Images for given night
images = Images.objects.extra(
select={
'filter_string': 'get_filter_name(filter)'
}).order_by('-time').filter(night=night)
query_type = 'night'
else:
images = Images.objects.extra(
select={
'filter_string': 'get_filter_name(filter)'
}).order_by('-time')
query_type = 'all'
if type and type != 'all':
images = images.filter(type=type)
else:
type = 'all'
if request.method == 'GET':
if request.GET.get('channel'):
images = images.filter(channel_id=int(request.GET.get('channel')))
if request.GET.get('filter'):
images = images.filter(filter__name=request.GET.get('filter'))
types = [
i[0]
for i in db_query("SELECT fast_distinct(%s, %s)", ('images', 'type'),
simplify=False)
]
types.append('all')
channels = [str(x) for x in range(1, settings.NCHANNELS + 1)]
return TemplateResponse(request,
'images.html',
context={
'images': images,
'night': night,
'type': type,
'types': types,
'query_type': query_type,
'channels': channels,
'ra': ra,
'dec': dec,
'sr': sr
})
def scheduler_target_view(request, id=0):
target = SchedulerTargets.objects.get(id=id)
context = {'target': target}
if request.method == 'POST':
action = request.POST.get('action')
if action == 'disable' and target.status.name == 'active':
target.status = SchedulerTargetStatus.objects.get(name='inactive')
target.save()
if action == 'enable' and target.status.name == 'inactive':
target.status = SchedulerTargetStatus.objects.get(name='active')
target.save()
if action == 'complete' and target.status.name != 'archived':
target.status = SchedulerTargetStatus.objects.get(name='completed')
target.save()
if action == 'restart':
target.status = SchedulerTargetStatus.objects.get(name='active')
target.save()
if action == 'delete':
target.delete()
if action == 'update':
name = request.POST.get('new-name')
coords = request.POST.get('new-coords')
type = request.POST.get('new-type')
filter = request.POST.get('new-filter')
# Parse exposure
try:
exposure = float(request.POST.get('new-exposure'))
exposure = max(0.1, min(exposure, 10000.0))
except:
exposure = 10.0
# Repeat
try:
repeat = int(request.POST.get('new-repeat'))
repeat = max(1, min(repeat, 1000))
except:
repeat = 1
# Remove whitespaces
name = '_'.join(name.split())
# Parse coordinates
sname, ra, dec = resolve(coords)
if not sname:
message = "Can't resolve object: %s" % (coords)
elif not name:
message = "Empty target name"
else:
target.name = name
target.type = type
target.filter = filter
target.exposure = exposure
target.repeat = repeat
target.ra = ra
target.dec = dec
target.save()
return redirect('scheduler_target', id)
uuid = target.uuid
images = Images.objects.raw(
"select *,get_filter_name(filter) as filter_string from images where keywords->'TARGET UUID'='%s' and type != 'avg' order by time desc"
% (uuid))
nimages = len(list(images))
context['images'] = images
context['nimages'] = nimages
return TemplateResponse(request, 'scheduler_target.html', context=context)
def alembic():
return resolve('alembic.config:main')()
def Resolve(tree, GeneToSpecies):
StoreSpeciesSets(tree, GeneToSpecies)
for n in tree.traverse("postorder"):
tree = resolve.resolve(n, GeneToSpecies)
return tree
string += '\n\t\t],\n'
for k in self.set_required_pre:
string += '\t\t"%s": [\n' %(dico[k + "Adjust"]) #ici
for c in self.alphabet:
fmt = '\t\t\t{ "read" : "%s", "to_state": "%s", "write": "%s", "action": "%s"},\n'
string += fmt %(c, dico[k], c, 'RIGHT') #ici
string = string[:-2]
string += '\n\t\t],\n'
string = string[:-2]
string += '\n\t}\n'
string += "}\n"
with open("lol.json", "w") as stream:
stream.write(string)
# print string
if __name__ == "__main__":
tk = get_tokens()
p = Prog(tk)
print p.name
print p.alphabet
print p.blank
print p.set_lb
for st in p.lst_st:
print str(st)
resolve(p)
p.tojson()
import json
import requests
from resolve import resolve
from jsonfind import find_and_modify
if __name__ == '__main__':
response = requests.get('http://localhost:5000')
body = response.json()
print(
f'response body: {json.dumps(body["container"]["params"], indent=4)}')
for resolver in body['resolvers']:
value = resolve(resolver, resolver['target']['type'])
find_and_modify(resolver['target']['query'],
body['container']['params'], value)
print(
f'resolved body: {json.dumps(body["container"]["params"], indent=4)}')
#建立数据库中的表单
def create_mysql():
key = [u'中文名称']
url = item_url + '1'
soup = BeautifulSoup(spider(url))
table = soup.html.body.findChildren('table')
tr = table[2].findChildren('tr')
for i in range(len(tr)):
td = tr[i].findChildren('td')
key.append(td[0].contents[0].split('\n')[0])
sql_create = """create table tcmcenter.tcm( tcmid int not null auto_increment,"""
for i in range(len(key) - 1):
sql_create = sql_create + key[i] + ' text null,'
sql_create = sql_create + key[-1] + " text null,primary key(tcmid));"
#print sql_create
cur.execute(sql_create)
#设置成MyISAM的形式,但是创建的时候默认是InnoDB，这么做的主要目的是使用InnoDB时不允许row size太大
sql_alter = """alter table tcmcenter.tcm engine=MyISAM"""
cur.execute(sql_alter)
conn.commit()
if __name__ == '__main__':
create_mysql()
for i in range(100):
url = item_url + str(i + 1)
resolve(spider(url))
cur.close()
conn.close()
def alembic():
return resolve('alembic.config:main')()
def main():
tar = None
if "M" in options.debug:
import pdb
pdb.set_trace()
if not options.filelist:
if options.archive:
tar = tarfile.open(options.archive)
options.filelist = tar.getnames()
elif options.code:
tmp = tempfile.NamedTemporaryFile(suffix=".m")
tmp.file.write(options.code)
tmp.file.flush()
options.filelist = [tmp.name]
if options.output:
print "Conflicting options -c and -o"
return
options.output = "-"
else:
options.parser.print_help()
return
if options.output == "-":
fp = sys.stdout
elif options.output:
fp = open(options.output, "w")
else:
fp = None
if fp:
print_header(fp)
if options.glob_pattern:
options.filelist = fnmatch.filter(options.filelist,
options.glob_pattern)
nerrors = 0
for i, options.filename in enumerate(options.filelist):
try:
if options.verbose:
print i, options.filename
if not options.filename.endswith(".m"):
if options.verbose:
print("\tIgnored: '%s' (unexpected file type)" %
options.filename)
continue
if basename(options.filename) in options.xfiles:
if options.verbose:
print "\tExcluded: '%s'" % options.filename
continue
if tar:
buf = tar.extractfile(options.filename).read()
else:
buf = open(options.filename).read()
buf = buf.replace("\r\n", "\n")
buf = buf.decode("ascii", errors="ignore")
stmt_list = parse.parse(buf if buf[-1] == '\n' else buf + '\n')
#assert None not in stmt_list
if not stmt_list:
continue
if not options.no_resolve:
G = resolve.resolve(stmt_list)
if not options.no_backend:
s = backend.backend(stmt_list)
if not options.output:
f = splitext(basename(options.filename))[0] + ".py"
with open(f, "w") as fp:
print_header(fp)
fp.write(s)
try:
py_compile.compile(f,doraise=True)
if options.execfile:
execfile(f)
except:
if options.delete-on-error:
os.unlink(f)
if options.verbose:
print "Removed",f
raise
else:
fp.write(s)
except KeyboardInterrupt:
break
except:
nerrors += 1
traceback.print_exc(file=sys.stdout)
if options.strict:
break
finally:
print "Errors:", nerrors
buf = buf[:-1] + "\n" + raw_input("... ")
if buf[0] == '?':
print main.__doc__
continue
if buf[0] == "!":
try:
exec buf[1:]
except Exception as ex:
print ex
continue
t = parse.parse(buf if buf[-1]=='\n' else buf+'\n')
if not t:
continue
print "t=", repr(t)
print 60*"-"
resolve.resolve(t,symtab)
print "t=", repr(t)
print 60*"-"
print "symtab:",symtab
s = backend.backend(t)
print "python:",s.strip()
try:
print eval(s)
except SyntaxError:
exec s
except EOFError:
return
except Exception as ex:
print ex
if not output:
def pscheduler():
return resolve('pyramid_scheduler.pscheduler:main')()
string = string[:-2]
string += '\n\t\t],\n'
for k in self.set_required_pre:
string += '\t\t"%s": [\n' % (dico[k + "Adjust"]) #ici
for c in self.alphabet:
fmt = '\t\t\t{ "read" : "%s", "to_state": "%s", "write": "%s", "action": "%s"},\n'
string += fmt % (c, dico[k], c, 'RIGHT') #ici
string = string[:-2]
string += '\n\t\t],\n'
string = string[:-2]
string += '\n\t}\n'
string += "}\n"
with open("lol.json", "w") as stream:
stream.write(string)
# print string
if __name__ == "__main__":
tk = get_tokens()
p = Prog(tk)
print p.name
print p.alphabet
print p.blank
print p.set_lb
for st in p.lst_st:
print str(st)
resolve(p)
p.tojson()
def start(self):
if not os.path.exists("/var/log/cronus"):
os.makedirs("/var/log/cronus")
logger_error = logging.getLogger("error_log")
eh = logging.FileHandler("/var/log/cronus/error.log")
eh.setLevel(logging.DEBUG)
logger_error.addHandler(eh)
logger_activity = logging.getLogger("activity_log")
ah = logging.FileHandler("/var/log/cronus/activity.log")
ah.setLevel(logging.DEBUG)
logger_activity.addHandler(ah)
while 1:
conn = MySQLdb.connect(host=config.dbhost, user=config.dbuser, passwd=config.dbpasswd, db=config.dbname)
cursor = conn.cursor()
# retrieve new jobs
cursor.execute("SELECT * from job_queue WHERE status = 0")
conn.commit()
conn.close()
job_rows = cursor.fetchall()
if len(job_rows) == 0:
print "No jobs"
else:
# seperate jobs that should be executed and discarded
job_rows, discarded_rows = resolve.resolve(job_rows)
print "No of resolved rows", len(job_rows)
print "No if discarded rows", len(discarded_rows)
# set the executable job's status to 1 and invokes JobHandler.
# updates the job in the db to prevent QueueHandler picking the job again
for job_row in job_rows:
job_id = job_row[0]
status = 1
deployment_sets = self.get_deployment_sets(job_id)
job = Job(job_id, status, deployment_sets)
conn = MySQLdb.connect(
host=config.dbhost, user=config.dbuser, passwd=config.dbpasswd, db=config.dbname
)
cursor = conn.cursor()
cursor.execute("UPDATE job_queue SET status = 1 WHERE id = " + str(job_id))
conn.commit()
conn.close()
jobhandler = JobHandler(job)
jobhandler.start()
# set the discarded job's status to 4 and invokes JobHandler
# updates the job in the db to prevent QueueHandler picking the job again
for job_row in discarded_rows:
job_id = job_row[0]
status = 4
deployment_sets = self.get_deployment_sets(job_id)
job = Job(job_id, status, deployment_sets)
conn = MySQLdb.connect(
host=config.dbhost, user=config.dbuser, passwd=config.dbpasswd, db=config.dbname
)
cursor = conn.cursor()
cursor.execute("UPDATE job_queue SET status = 1 WHERE id = " + str(job_id))
conn.commit()
conn.close()
jobhandler = JobHandler(job)
jobhandler.start()
time.sleep(60)
def main():
if "M" in options.debug:
import pdb
pdb.set_trace()
if not options.filelist:
options.parser.print_help()
return
if options.output == "-":
fp = sys.stdout
elif options.output:
fp = open(options.output, "w")
else:
fp = None
nerrors = 0
for i, options.filename in enumerate(options.filelist):
try:
if options.verbose:
print(i, options.filename)
if not options.filename.endswith(".m"):
print("\tIgnored: '%s' (unexpected file type)" %
options.filename)
continue
if basename(options.filename) in options.xfiles:
if options.verbose:
print("\tExcluded: '%s'" % options.filename)
continue
buf = open(options.filename).read()
buf = buf.replace("\r\n", "\n")
stmt_list = parse.parse(buf if buf[-1] == '\n' else buf + '\n')
if not stmt_list:
continue
if not options.no_resolve:
G = resolve.resolve(stmt_list)
graph_list = []
for n in G.nodes():
temp = str.split(n, '_')
while len(temp) > 3:
temp[0] += '_' + temp.pop(1)
graph_list.append(temp + [G.node[n]["ident"].props])
resolve_array_refs(stmt_list, graph_list)
#print_list(stmt_list)
if not options.no_backend:
s = backend.backend(stmt_list).strip()
if not options.output:
f = splitext(basename(options.filename))[0] + ".py"
with open(f, "w") as fp:
print_header(fp, s)
fp.write(s)
else:
print_header(fp, s)
fp.write(s)
except KeyboardInterrupt:
break
except:
nerrors += 1
traceback.print_exc(file=sys.stdout)
if options.strict:
break
finally:
pass
if nerrors:
print("Errors:", nerrors)
def proxy(argv=sys.argv):
pcmd = argv[0][argv[0].rindex('i-') + 2:]
return resolve('pyramid.scripts.' + pcmd + ':main')(argv=argv)
def main():
#args = options.parser.parse_args()
#for key in dir(args):
# if not key.startswith("_"):
# setattr(options,key,getattr(args,key))
if not options.filelist:
options.parser.print_help()
return
#assert options.filelist
#xfiles = options.exclude.split(",") if options.exclude else []
if not options.output:
options.output = "a.py"
fp = open(options.output,"w") if options.output != "-" else sys.stdout
print >> fp, "# Autogenerated with SMOP "# + options.version
# for key in dir(options.args):
# if not key.startswith("_"):
# value = getattr(options,key)
# print >> fp, '# %s=%s' % (key,value)
print >> fp, "from __future__ import division"
print >> fp, "from core import *"
#if options.callgraph:
# C = nx.DiGraph()
for options.filename in options.filelist:
try:
#for options.filename in glob.glob(os.path.expanduser(pattern)):
print >> fp, "#", options.filename
if not options.filename.endswith((".m",".tst")):
print "\tIgnored file: '%s'" % options.filename
continue
if os.path.basename(options.filename) in options.xfiles:
print "\tExcluded file: '%s'" % options.filename
continue
if options.verbose:
print options.filename
buf = open(options.filename).read().replace("\r\n","\n")
stmt_list=parse.parse(buf if buf[-1]=='\n' else buf+'\n')
#assert None not in stmt_list
if not stmt_list and options.strict:
return
if options.enumerate:
for i,stmt_obj in enumerate(stmt_list):
#stmt_class = stmt_obj.__class__.__name__
print i, stmt_obj
# if i == options.debug_index:
# import pdb ; pdb.set_trace()
# if stmt_class == "func_stmt":
# func_name = stmt_obj.ident.name
# if options.verbose:
# print "\t",func_name
# else:
# func_name = ""
if not options.no_resolve:
G = resolve.resolve(stmt_list)
if not options.no_backend:
s = backend.backend(stmt_list)
print >> fp, s
except Exception as e:
print e
if options.strict:
raise
def scheduler_targets_list(request, type=None):
message = None
inactive = False
active = True
completed = True
archived = False
failed = False
if request.method == 'POST':
message = ""
ids = [int(id) for id in request.POST.getlist('target_ids[]')]
action = request.POST.get('action')
# message += request.POST.__str__()
# if message:
# message += "<br>"
if action == 'new':
name = request.POST.get('new-name')
coords = request.POST.get('new-coords')
type = request.POST.get('new-type')
filter = request.POST.get('new-filter')
# Parse exposure
try:
exposure = float(request.POST.get('new-exposure'))
exposure = max(0.1, min(exposure, 10000.0))
except:
exposure = 10.0
# Repeat
try:
repeat = int(request.POST.get('new-repeat'))
repeat = max(1, min(repeat, 1000))
except:
repeat = 1
# Remove whitespaces
name = '_'.join(name.split())
# Parse coordinates
sname, ra, dec = resolve(coords)
if not sname:
message = "Can't resolve object: %s" % (coords)
elif not name:
message = "Empty target name"
else:
id = db_query(
"INSERT INTO scheduler_targets (name, type, ra, dec, exposure, repeat, filter, status, time_created)"
+
" VALUES (%s, %s, %s, %s, %s, %s, %s, get_scheduler_target_status_id('active'), favor2_timestamp()) RETURNING id",
(name, type, ra, dec, exposure, repeat, filter))
message = "Target %d created: Name: %s RA: %g Dec: %g Type: %s Filter: %s Exp: %g Repeat: %d" % (
id, name, ra, dec, type, filter, exposure, repeat)
elif len(ids):
for id in ids:
target = SchedulerTargets.objects.get(id=id)
if action == 'disable' and target.status.name == 'active':
target.status = SchedulerTargetStatus.objects.get(
name='inactive')
target.save()
message += "Target %d disabled<br>" % id
if action == 'enable' and target.status.name == 'inactive':
target.status = SchedulerTargetStatus.objects.get(
name='active')
target.save()
message += "Target %d enabled<br>" % id
if action == 'complete' and target.status.name != 'archived':
target.status = SchedulerTargetStatus.objects.get(
name='completed')
target.save()
message += "Target %d completed<br>" % id
if action == 'restart':
target.status = SchedulerTargetStatus.objects.get(
name='active')
target.save()
message += "Target %d restarted<br>" % id
if action == 'delete':
target.delete()
message += "Target %d deleted<br>" % id
else:
message = "No targets selected"
# Redirect to the same view, but with no POST args. We can't display messages with it!
return redirect('scheduler_targets')
elif request.method == 'GET':
active = int(request.GET.get('active', active))
inactive = int(request.GET.get('inactive', inactive))
completed = int(request.GET.get('completed', completed))
failed = int(request.GET.get('failed', failed))
type = request.GET.get('type', type)
targets = SchedulerTargets.objects.order_by('-time_created')
if not active:
targets = targets.exclude(status__name='active')
if not inactive:
targets = targets.exclude(status__name='inactive')
if not completed:
targets = targets.exclude(status__name='completed')
if not archived:
targets = targets.exclude(status__name='archived')
if not failed:
targets = targets.exclude(status__name='failed')
if type and type != 'all':
targets = targets.filter(type=type)
else:
type = 'all'
context = {
'targets': targets,
'message': message,
'type': type,
'active': active,
'inactive': inactive,
'completed': completed,
'archived': archived,
'failed': failed
}
context['types'] = [
_['type']
for _ in SchedulerTargets.objects.distinct('type').values('type')
]
context['types'].append('all')
return TemplateResponse(request, 'scheduler_targets.html', context=context)
args = parser.parse_args()
#print("The arguments given are: ")
#print("Genome is",args.genome_file)
#print("VCF File is", args.vcf_file)
#print("MEI Annotation file is", args.annot_file)
#print("Output File is", args.output_file)7
vcf_new = ''
if args.vcf_folder is None:
if args.output_file is None:
output = args.vcf_file + "_v2"
vcf_new = open(output, "w")
else:
output = args.output_file
vcf_new = open(output, "w")
if args.resolve:
if args.annot_file is None or args.genome_file is None:
sys.exit('Please run with correct genome and annotation file')
else:
mei_annot_file = args.annot_file
genome = args.genome_file
rslv.resolve(genome, args.vcf_file, vcf_new, mei_annot_file,
args.precise, args.vcf_folder, args.verbose)
elif args.mendelian:
print(
"Running mendelian filter (Make sure that your VCF has the required columns for the trio and son must be at the last column)"
)
mf.flt(args.vcf_file, vcf_new)