def _parse_flags(self, cmd_flag_map, args):
"""Expects arguments after the initial command and subcommands (i.e.,
the second item returned from _parse_subcmds)
Returns a tuple of (multidict of flag names to parsed and validated values, remaining_args).
Raises on unknown subcommands.
"""
flag_value_map = OMD()
ff_path_res_map = OrderedDict()
ff_path_seen = set()
orig_args = args
while args:
arg = args[0]
if not arg or arg[0] != '-' or arg == '-' or arg == '--':
# posargs or post_posargs beginning ('-' is a conventional pos arg for stdin)
break
flag, value, args = self._parse_single_flag(cmd_flag_map, args)
flag_value_map.add(flag.name, value)
if flag is self.flagfile_flag:
self._parse_flagfile(cmd_flag_map,
value,
res_map=ff_path_res_map)
for path, ff_flag_value_map in ff_path_res_map.items():
if path in ff_path_seen:
continue
flag_value_map.update_extend(ff_flag_value_map)
ff_path_seen.add(path)
return flag_value_map, ff_path_res_map, args
class EventEmitter2(object):
def __init__(self):
"""
"""
self.events = OrderedMultiDict()
self.on = self.add_listener
self.off = self.remove_listener
# TODO: Add listener to remove
def add_listener(self, event, listener, count=0):
if not (isinstance(listener, FunctionType)) or (isinstance(listener, BuiltinFunctionType)):
raise Exception("Invalid Listener: %s" % (str(listener)))
_event = re.compile(event)
_listener = {"handler": listener, "calls": 0, "calls_left": count}
self.events.add(_event, _listener)
return True
def emit(self, event, kwargs):
for pattern, listener in self.events.iteritems(multi=True):
if pattern.match(event):
if not listener["calls_left"]:
log.debug("Removing Listener: %s on Pattern: %s") % (
listener, pattern)
self.remove_listener(pattern, listener)
listener["calls"] += 1
listener["calls_left"] -= 1
yield listener["handler"](**kwargs)
def remove_listener(self, pattern, listener):
pattern = re.compile(pattern)
listeners = self.events.getlist(pattern)
for pattern, _listener in self.events.iteritems(multi=True):
if _listener['handler'] == listener:
listener = _listener
break
listeners = self.events.getlist(pattern)
listeners.remove(listener)
if len(listeners):
self.events.update({pattern: listeners})
else:
self.events._remove(pattern)
return True
def on_any(self, listener):
raise NotImplementedError
def off_any(self, listener):
raise NotImplementedError
def once(self, event, listener):
self.add_listener(event, listener, left=1)
def many(self, event, listener, left):
self.add_listener(event, listener, left)
class EventEmitter2(object):
def __init__(self):
"""
"""
self.events = OrderedMultiDict()
self.on = self.add_listener
self.off = self.remove_listener
# TODO: Add listener to remove
def add_listener(self, event, listener, count=0):
if (isinstance(listener, BuiltinFunctionType)):
raise Exception("Invalid Listener: %s" % (str(listener)))
_event = re.compile(event)
_listener = {"handler": listener, "calls": 0, "calls_left": count}
self.events.add(_event, _listener)
return True
def emit(self, event, kwargs):
for pattern, listener in self.events.iteritems(multi=True):
if pattern.match(event):
if not listener["calls_left"]:
log.debug("Removing Listener: %s on Pattern: %s") % (
listener, pattern)
self.remove_listener(pattern, listener)
listener["calls"] += 1
listener["calls_left"] -= 1
yield listener["handler"](**kwargs)
def remove_listener(self, pattern, listener):
pattern = re.compile(pattern)
listeners = self.events.getlist(pattern)
for pattern, _listener in self.events.iteritems(multi=True):
if _listener['handler'] == listener:
listener = _listener
break
listeners = self.events.getlist(pattern)
listeners.remove(listener)
if len(listeners):
self.events.update({pattern: listeners})
else:
self.events._remove(pattern)
return True
def on_any(self, listener):
raise NotImplementedError
def off_any(self, listener):
raise NotImplementedError
def once(self, event, listener):
self.add_listener(event, listener, left=1)
def many(self, event, listener, left):
self.add_listener(event, listener, left)
def read_instructions() -> OrderedMultiDict[str, str]:
instructions = OrderedMultiDict()
instruction_regex = re.compile(r"\s(\w)\s")
with open(INPUT_FILE, "r") as f_handle:
for line in f_handle:
if line:
key, value = instruction_regex.findall(line.rstrip())
if key not in instructions:
instructions[key] = value
else:
instructions.add(key, value)
return instructions
def analyze_samples():
outcome = OrderedMultiDict()
opcode = Opcode()
methods = [
func
for func in getmembers(Opcode, predicate=isfunction)
if func[0] != "__init__"
]
count = 0
for before, instruction, after in read_inputs():
outcome.clear()
for opcode_method in methods:
if getattr(opcode, opcode_method[0])(before, instruction) == after:
outcome.add(instruction[0], opcode_method[0])
if len(outcome.getlist(instruction[0])) >= 3:
count += 1
#print(outcome)
print(count)
def epi_suite_values(epi_blob):
'''Extracts some information as key-value pairs from EPI Suite output.
Pretty rough (work in progress).'''
data = OMD()
try:
lines = epi_blob.split('\n')
for i in lines:
j = i.strip()
if j.startswith('Log Kow (') or j.startswith('Log BCF'):
data.update(dict_from_line(i, '='))
if j.startswith('Henrys LC') or\
j.startswith('Log Koa (KOAWIN') or\
j.startswith('Log Koa (experimental') or\
j.startswith('Ready Biodegradability Prediction'):
data.update(dict_from_line(i))
if 'Fugacity' in epi_blob:
model_table = epi_blob.split('Level III Fugacity Model:', 1)[1]
data.add('Level III Fugacity Model', model_table)
except:
pass
return data
def cs_scrape_properties(csid, props=None):
'''Retrieve some of the experimental and predicted chemical properties that
are not surfaced in the ChemSpider web API.'''
try:
r = requests.get('http://www.chemspider.com/Chemical-Structure.{0}.html'.format(csid))
r.raise_for_status()
except Exception as e:
print(e)
return None
data = OMD([('CSID', csid)])
doc = BeautifulSoup(r.text, 'lxml')
# Experimental and predicted properties ("Experimental data" tab):
props_tabs = doc.find(id='suppInfoTab')
try:
props_found = props_tabs.find_all(class_='user_data_property_name')
for p in props_found:
prop_name = p.get_text().strip(': \r\n')
if props is not None and prop_name not in props:
continue
li = p.find_parent('li')
values = li.find_all('td')
for i in values:
value = i.get_text().strip()
data.add(prop_name, value)
except AttributeError:
pass
# ACD/Labs predicted properties:
acd_tab = doc.find(id='acdLabsTab')
try:
acd_props = acd_tab.find_all(class_='prop_title')
for p in acd_props:
prop_name = p.get_text().strip(': \r\n')
v = p.find_next_sibling('td')
value = v.get_text().strip()
if props is not None and prop_name not in props:
continue
# Make sure all predicted properties are obviously named
if prop_name.startswith('ACD/') is False:
prop_name = 'ACD/' + prop_name
data.add(prop_name, value)
except AttributeError:
pass
# EPI Suite results, as a blob to process later:
# Sometimes only returns part of the text, for some reason.
if props is not None and 'EPI Suite' not in props:
pass
else:
epi_tab = doc.find(id='epiTab')
epi_blob = epi_tab.get_text().strip() if epi_tab else None
data.add('EPI Suite', epi_blob)
return data
