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<SYSTEM_TASK:>
Injects the block start and end times
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Description:
def extend_schema_spec(self) -> None:
""" Injects the block start and end times """ |
super().extend_schema_spec()
if self.ATTRIBUTE_FIELDS in self._spec:
# Add new fields to the schema spec. Since `_identity` is added by the super, new elements are added after
predefined_field = self._build_time_fields_spec(self._spec[self.ATTRIBUTE_NAME])
self._spec[self.ATTRIBUTE_FIELDS][1:1] = predefined_field
# Add new field schema to the schema loader
for field_schema in predefined_field:
self.schema_loader.add_schema_spec(field_schema, self.fully_qualified_name) |
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Builds an expression object. Adds an error if expression creation has errors.
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Description:
def build_expression(self, attribute: str) -> Optional[Expression]:
""" Builds an expression object. Adds an error if expression creation has errors. """ |
expression_string = self._spec.get(attribute, None)
if expression_string:
try:
return Expression(str(expression_string))
except Exception as err:
self.add_errors(
InvalidExpressionError(self.fully_qualified_name, self._spec, attribute, err))
return None |
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Adds errors to the error repository in schema loader
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Description:
def add_errors(self, *errors: Union[BaseSchemaError, List[BaseSchemaError]]) -> None:
""" Adds errors to the error repository in schema loader """ |
self.schema_loader.add_errors(*errors) |
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Validates that the schema contains a series of required attributes
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Description:
def validate_required_attributes(self, *attributes: str) -> None:
""" Validates that the schema contains a series of required attributes """ |
self.add_errors(
validate_required_attributes(self.fully_qualified_name, self._spec, *attributes)) |
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Validates that the attribute contains a numeric value within boundaries if specified
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Description:
def validate_number_attribute(self,
attribute: str,
value_type: Union[Type[int], Type[float]] = int,
minimum: Optional[Union[int, float]] = None,
maximum: Optional[Union[int, float]] = None) -> None:
""" Validates that the attribute contains a numeric value within boundaries if specified """ |
self.add_errors(
validate_number_attribute(self.fully_qualified_name, self._spec, attribute, value_type,
minimum, maximum)) |
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Validates that the attribute value is among the candidates
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Description:
def validate_enum_attribute(self, attribute: str,
candidates: Set[Union[str, int, float]]) -> None:
""" Validates that the attribute value is among the candidates """ |
self.add_errors(
validate_enum_attribute(self.fully_qualified_name, self._spec, attribute, candidates)) |
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Implements snapshot for collections by recursively invoking snapshot of all child items
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Description:
def _snapshot(self) -> Dict[str, Any]:
"""
Implements snapshot for collections by recursively invoking snapshot of all child items
""" |
try:
return {name: item._snapshot for name, item in self._nested_items.items()}
except Exception as e:
raise SnapshotError('Error while creating snapshot for {}'.format(self._name)) from e |
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Restores the state of a collection from a snapshot
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Description:
def run_restore(self, snapshot: Dict[Union[str, Key], Any]) -> 'BaseItemCollection':
"""
Restores the state of a collection from a snapshot
""" |
try:
for name, snap in snapshot.items():
if isinstance(name, Key):
self._nested_items[name.group].run_restore(snap)
else:
self._nested_items[name].run_restore(snap)
return self
except Exception as e:
raise SnapshotError('Error while restoring snapshot: {}'.format(self._snapshot)) from e |
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Executes the streaming and window BTS on the given records. An option old state can provided
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Description:
def execute_per_identity_records(
self,
identity: str,
records: List[TimeAndRecord],
old_state: Optional[Dict[Key, Any]] = None) -> Tuple[str, Tuple[Dict, List]]:
"""
Executes the streaming and window BTS on the given records. An option old state can provided
which initializes the state for execution. This is useful for batch execution where the
previous state is written out to storage and can be loaded for the next batch run.
:param identity: Identity of the records.
:param records: List of TimeAndRecord to be processed.
:param old_state: Streaming BTS state dictionary from a previous execution.
:return: Tuple[Identity, Tuple[Identity, Tuple[Streaming BTS state dictionary,
List of window BTS output]].
""" |
schema_loader = SchemaLoader()
if records:
records.sort(key=lambda x: x[0])
else:
records = []
block_data = self._execute_stream_bts(records, identity, schema_loader, old_state)
window_data = self._execute_window_bts(identity, schema_loader)
return identity, (block_data, window_data) |
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String representation with additional information
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Description:
def to_string(self, hdr, other):
"""String representation with additional information""" |
result = "%s[%s,%s" % (
hdr, self.get_type(self.type), self.get_clazz(self.clazz))
if self.unique:
result += "-unique,"
else:
result += ","
result += self.name
if other is not None:
result += ",%s]" % (other)
else:
result += "]"
return result |
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Returns true if the question is answered by the record
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Description:
def answered_by(self, rec):
"""Returns true if the question is answered by the record""" |
return self.clazz == rec.clazz and \
(self.type == rec.type or self.type == _TYPE_ANY) and \
self.name == rec.name |
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Sets this record's TTL and created time to that of
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Description:
def reset_ttl(self, other):
"""Sets this record's TTL and created time to that of
another record.""" |
self.created = other.created
self.ttl = other.ttl |
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String representation with addtional information
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Description:
def to_string(self, other):
"""String representation with addtional information""" |
arg = "%s/%s,%s" % (
self.ttl, self.get_remaining_ttl(current_time_millis()), other)
return DNSEntry.to_string(self, "record", arg) |
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Update only one property in the dict
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Description:
def set_property(self, key, value):
"""
Update only one property in the dict
""" |
self.properties[key] = value
self.sync_properties() |
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Reads header portion of packet
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Description:
def read_header(self):
"""Reads header portion of packet""" |
format = '!HHHHHH'
length = struct.calcsize(format)
info = struct.unpack(format,
self.data[self.offset:self.offset + length])
self.offset += length
self.id = info[0]
self.flags = info[1]
self.num_questions = info[2]
self.num_answers = info[3]
self.num_authorities = info[4]
self.num_additionals = info[5] |
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Reads questions section of packet
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Description:
def read_questions(self):
"""Reads questions section of packet""" |
format = '!HH'
length = struct.calcsize(format)
for i in range(0, self.num_questions):
name = self.read_name()
info = struct.unpack(format,
self.data[self.offset:self.offset + length])
self.offset += length
question = DNSQuestion(name, info[0], info[1])
self.questions.append(question) |
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Reads an integer from the packet
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Description:
def read_int(self):
"""Reads an integer from the packet""" |
format = '!I'
length = struct.calcsize(format)
info = struct.unpack(format,
self.data[self.offset:self.offset + length])
self.offset += length
return info[0] |
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Reads a character string from the packet
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Description:
def read_character_string(self):
"""Reads a character string from the packet""" |
length = ord(self.data[self.offset])
self.offset += 1
return self.read_string(length) |
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Reads a string of a given length from the packet
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Description:
def read_string(self, len):
"""Reads a string of a given length from the packet""" |
format = '!' + str(len) + 's'
length = struct.calcsize(format)
info = struct.unpack(format,
self.data[self.offset:self.offset + length])
self.offset += length
return info[0] |
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Reads the answers, authorities and additionals section
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Description:
def read_others(self):
"""Reads the answers, authorities and additionals section
of the packet""" |
format = '!HHiH'
length = struct.calcsize(format)
n = self.num_answers + self.num_authorities + self.num_additionals
for i in range(0, n):
domain = self.read_name()
info = struct.unpack(format,
self.data[self.offset:self.offset + length])
self.offset += length
rec = None
if info[0] == _TYPE_A:
rec = DNSAddress(domain,
info[0], info[1], info[2],
self.read_string(4))
elif info[0] == _TYPE_CNAME or info[0] == _TYPE_PTR:
rec = DNSPointer(domain,
info[0], info[1], info[2],
self.read_name())
elif info[0] == _TYPE_TXT:
rec = DNSText(domain,
info[0], info[1], info[2],
self.read_string(info[3]))
elif info[0] == _TYPE_SRV:
rec = DNSService(domain,
info[0], info[1], info[2],
self.read_unsigned_short(),
self.read_unsigned_short(),
self.read_unsigned_short(),
self.read_name())
elif info[0] == _TYPE_HINFO:
rec = DNSHinfo(domain,
info[0], info[1], info[2],
self.read_character_string(),
self.read_character_string())
elif info[0] == _TYPE_RRSIG:
rec = DNSSignatureI(domain,
info[0], info[1], info[2],
self.read_string(18),
self.read_name(),
self.read_character_string())
elif info[0] == _TYPE_AAAA:
rec = DNSAddress(domain,
info[0], info[1], info[2],
self.read_string(16))
else:
# Try to ignore types we don't know about
# this may mean the rest of the name is
# unable to be parsed, and may show errors
# so this is left for debugging. New types
# encountered need to be parsed properly.
#
#print "UNKNOWN TYPE = " + str(info[0])
#raise BadTypeInNameException
pass
if rec is not None:
self.answers.append(rec) |
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Reads a UTF-8 string of a given length from the packet
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Description:
def read_utf(self, offset, len):
"""Reads a UTF-8 string of a given length from the packet""" |
try:
result = self.data[offset:offset + len].decode('utf-8')
except UnicodeDecodeError:
result = str('')
return result |
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Reads a domain name from the packet
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Description:
def read_name(self):
"""Reads a domain name from the packet""" |
result = ''
off = self.offset
next = -1
first = off
while 1:
len = ord(self.data[off])
off += 1
if len == 0:
break
t = len & 0xC0
if t == 0x00:
result = ''.join((result, self.read_utf(off, len) + '.'))
off += len
elif t == 0xC0:
if next < 0:
next = off + 1
off = ((len & 0x3F) << 8) | ord(self.data[off])
if off >= first:
raise Exception(
"Bad domain name (circular) at " + str(off))
first = off
else:
raise Exception("Bad domain name at " + str(off))
if next >= 0:
self.offset = next
else:
self.offset = off
return result |
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Adds an answer if if does not expire by a certain time
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Description:
def add_answer_at_time(self, record, now):
"""Adds an answer if if does not expire by a certain time""" |
if record is not None:
if now == 0 or not record.is_expired(now):
self.answers.append((record, now))
if record.rrsig is not None:
self.answers.append((record.rrsig, now)) |
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Writes a single byte to the packet
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Description:
def write_byte(self, value):
"""Writes a single byte to the packet""" |
format = '!B'
self.data.append(struct.pack(format, value))
self.size += 1 |
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Inserts an unsigned short in a certain position in the packet
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Description:
def insert_short(self, index, value):
"""Inserts an unsigned short in a certain position in the packet""" |
format = '!H'
self.data.insert(index, struct.pack(format, value))
self.size += 2 |
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Writes an unsigned integer to the packet
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Description:
def write_int(self, value):
"""Writes an unsigned integer to the packet""" |
format = '!I'
self.data.append(struct.pack(format, int(value)))
self.size += 4 |
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Writes a string to the packet
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Description:
def write_string(self, value, length):
"""Writes a string to the packet""" |
format = '!' + str(length) + 's'
self.data.append(struct.pack(format, value))
self.size += length |
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Writes a UTF-8 string of a given length to the packet
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Description:
def write_utf(self, s):
"""Writes a UTF-8 string of a given length to the packet""" |
utfstr = s.encode('utf-8')
length = len(utfstr)
if length > 64:
raise NamePartTooLongException
self.write_byte(length)
self.write_string(utfstr, length) |
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Writes a domain name to the packet
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Description:
def write_name(self, name):
"""Writes a domain name to the packet""" |
try:
# Find existing instance of this name in packet
#
index = self.names[name]
except KeyError:
# No record of this name already, so write it
# out as normal, recording the location of the name
# for future pointers to it.
#
self.names[name] = self.size
parts = name.split('.')
if parts[-1] == '':
parts = parts[:-1]
for part in parts:
self.write_utf(part)
self.write_byte(0)
return
# An index was found, so write a pointer to it
#
self.write_byte((index >> 8) | 0xC0)
self.write_byte(index) |
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Writes a question to the packet
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Description:
def write_question(self, question):
"""Writes a question to the packet""" |
self.write_name(question.name)
self.write_short(question.type)
self.write_short(question.clazz) |
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Returns a string containing the packet's bytes
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Description:
def packet(self):
"""Returns a string containing the packet's bytes
No further parts should be added to the packet once this
is done.""" |
if not self.finished:
self.finished = 1
for question in self.questions:
self.write_question(question)
for answer, time in self.answers:
self.write_record(answer, time)
for authority in self.authorities:
self.write_record(authority, 0)
for additional in self.additionals:
self.write_record(additional, 0)
self.insert_short(0, len(self.additionals))
self.insert_short(0, len(self.authorities))
self.insert_short(0, len(self.answers))
self.insert_short(0, len(self.questions))
self.insert_short(0, self.flags)
if self.multicast:
self.insert_short(0, 0)
else:
self.insert_short(0, self.id)
return b''.join(self.data) |
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Gets an entry by key. Will return None if there is no
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Description:
def get(self, entry):
"""Gets an entry by key. Will return None if there is no
matching entry.""" |
try:
list = self.cache[entry.key]
return list[list.index(entry)]
except:
return None |
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Gets an entry by details. Will return None if there is
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Description:
def get_by_details(self, name, type, clazz):
"""Gets an entry by details. Will return None if there is
no matching entry.""" |
entry = DNSEntry(name, type, clazz)
return self.get(entry) |
<SYSTEM_TASK:>
Callback invoked by Zeroconf when new information arrives.
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Description:
def update_record(self, zeroconf, now, record):
"""Callback invoked by Zeroconf when new information arrives.
Updates information required by browser in the Zeroconf cache.""" |
if record.type == _TYPE_PTR and record.name == self.type:
expired = record.is_expired(now)
try:
oldrecord = self.services[record.alias.lower()]
if not expired:
oldrecord.reset_ttl(record)
else:
del(self.services[record.alias.lower()])
callback = lambda x: self.listener.remove_service(x,
self.type, record.alias)
self.list.append(callback)
return
except:
if not expired:
self.services[record.alias.lower()] = record
callback = lambda x: self.listener.add_service(x,
self.type, record.alias)
self.list.append(callback)
expires = record.get_expiration_time(75)
if expires < self.next_time:
self.next_time = expires |
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Sets properties and text of this info from a dictionary
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Description:
def set_properties(self, properties):
"""Sets properties and text of this info from a dictionary""" |
if isinstance(properties, dict):
self.properties = properties
self.sync_properties()
else:
self.text = properties |
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Sets properties and text given a text field
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Description:
def set_text(self, text):
"""Sets properties and text given a text field""" |
self.text = text
try:
self.properties = text_to_dict(text)
except:
traceback.print_exc()
self.properties = None |
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Updates service information from a DNS record
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Description:
def update_record(self, zeroconf, now, record):
"""Updates service information from a DNS record""" |
if record is not None and not record.is_expired(now):
if record.type == _TYPE_A:
if record.name == self.name:
if not record.address in self.address:
self.address.append(record.address)
elif record.type == _TYPE_SRV:
if record.name == self.name:
self.server = record.server
self.port = record.port
self.weight = record.weight
self.priority = record.priority
self.address = []
self.update_record(zeroconf, now,
zeroconf.cache.get_by_details(self.server,
_TYPE_A, _CLASS_IN))
elif record.type == _TYPE_TXT:
if record.name == self.name:
self.set_text(record.text) |
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Returns true if the service could be discovered on the
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Description:
def request(self, zeroconf, timeout):
"""Returns true if the service could be discovered on the
network, and updates this object with details discovered.
""" |
now = current_time_millis()
delay = _LISTENER_TIME
next = now + delay
last = now + timeout
result = 0
try:
zeroconf.add_listener(self,
DNSQuestion(self.name, _TYPE_ANY, _CLASS_IN))
while self.server is None or \
len(self.address) == 0 or \
self.text is None:
if last <= now:
return 0
if next <= now:
out = DNSOutgoing(_FLAGS_QR_QUERY)
out.add_question(DNSQuestion(self.name,
_TYPE_SRV, _CLASS_IN))
out.add_answer_at_time(
zeroconf.cache.get_by_details(self.name,
_TYPE_SRV, _CLASS_IN), now)
out.add_question(
DNSQuestion(self.name, _TYPE_TXT, _CLASS_IN))
out.add_answer_at_time(
zeroconf.cache.get_by_details(self.name,
_TYPE_TXT, _CLASS_IN), now)
if self.server is not None:
out.add_question(
DNSQuestion(self.server, _TYPE_A, _CLASS_IN))
out.add_answer_at_time(
zeroconf.cache.get_by_details(self.server,
_TYPE_A, _CLASS_IN), now)
zeroconf.send(out)
next = now + delay
delay = delay * 2
zeroconf.wait(min(next, last) - now)
now = current_time_millis()
result = 1
finally:
zeroconf.remove_listener(self)
return result |
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Calling thread waits for a given number of milliseconds or
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Description:
def wait(self, timeout):
"""Calling thread waits for a given number of milliseconds or
until notified.""" |
self.condition.acquire()
self.condition.wait(timeout // 1000)
self.condition.release() |
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Notifies all waiting threads
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Description:
def notify_all(self):
"""Notifies all waiting threads""" |
self.condition.acquire()
# python 3.x
try:
self.condition.notify_all()
except:
self.condition.notifyAll()
self.condition.release() |
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Returns network's service information for a particular
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Description:
def get_service_info(self, type, name, timeout=3000):
"""Returns network's service information for a particular
name and type, or None if no service matches by the timeout,
which defaults to 3 seconds.""" |
info = ServiceInfo(type, name)
if info.request(self, timeout):
return info
return None |
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Adds a listener for a particular service type. This object
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Description:
def add_serviceListener(self, type, listener):
"""Adds a listener for a particular service type. This object
will then have its update_record method called when information
arrives for that type.""" |
self.remove_service_listener(listener)
self.browsers.append(ServiceBrowser(self, type, listener)) |
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Removes a listener from the set that is currently listening.
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Description:
def remove_service_listener(self, listener):
"""Removes a listener from the set that is currently listening.""" |
for browser in self.browsers:
if browser.listener == listener:
browser.cancel()
del(browser) |
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Registers service information to the network with a default TTL
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Description:
def register_service(self, info):
"""Registers service information to the network with a default TTL
of 60 seconds. Zeroconf will then respond to requests for
information for that service. The name of the service may be
changed if needed to make it unique on the network.""" |
self.check_service(info)
self.services[info.name.lower()] = info
# zone transfer
self.transfer_zone(info.type)
self.announce_service(info.name) |
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Checks the network for a unique service name, modifying the
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Description:
def check_service(self, info):
"""Checks the network for a unique service name, modifying the
ServiceInfo passed in if it is not unique.""" |
now = current_time_millis()
next_time = now
i = 0
while i < 3:
for record in self.cache.entries_with_name(info.type):
if record.type == _TYPE_PTR and \
not record.is_expired(now) and \
record.alias == info.name:
if (info.name.find('.') < 0):
info.name = info.name + ".[" + \
info.address + \
":" + info.port + \
"]." + info.type
self.check_service(info)
return
raise NonUniqueNameException
if now < next_time:
self.wait(next_time - now)
now = current_time_millis()
continue
out = DNSOutgoing(_FLAGS_QR_QUERY | _FLAGS_AA)
self.debug = out
out.add_question(
DNSQuestion(info.type, _TYPE_PTR, _CLASS_IN))
out.add_authorative_answer(
DNSPointer(info.type,
_TYPE_PTR, _CLASS_IN, info.ttl, info.name))
self.send(out)
i += 1
next_time += _CHECK_TIME |
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Adds a listener for a given question. The listener will have
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Description:
def add_listener(self, listener, question):
"""Adds a listener for a given question. The listener will have
its update_record method called when information is available to
answer the question.""" |
now = current_time_millis()
self.listeners.append(listener)
if question is not None:
for record in self.cache.entries_with_name(question.name):
if question.answered_by(record) and not record.is_expired(now):
listener.update_record(self, now, record)
self.notify_all() |
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Used to notify listeners of new information that has updated
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Description:
def update_record(self, now, rec):
"""Used to notify listeners of new information that has updated
a record.""" |
for listener in self.listeners:
listener.update_record(self, now, rec)
self.notify_all() |
<SYSTEM_TASK:>
Deal with incoming response packets. All answers
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Description:
def handle_response(self, msg, address):
"""Deal with incoming response packets. All answers
are held in the cache, and listeners are notified.""" |
now = current_time_millis()
sigs = []
precache = []
for record in msg.answers:
if isinstance(record, DNSSignature):
sigs.append(record)
else:
precache.append(record)
for e in precache:
for s in sigs:
if self.verify(e, s):
# print "DNS: %s verified with %s" % (e,s)
if self.adaptive and e.type == _TYPE_A:
if e.address == '\x00\x00\x00\x00':
e.address = socket.inet_aton(address)
if e in self.cache.entries():
if e.is_expired(now):
for i in self.hooks:
try:
i.remove(e)
except:
pass
self.cache.remove(e)
self.cache.remove(s)
else:
entry = self.cache.get(e)
sig = self.cache.get(s)
if (entry is not None) and (sig is not None):
for i in self.hooks:
try:
i.update(e)
except:
pass
entry.reset_ttl(e)
sig.reset_ttl(s)
else:
e.rrsig = s
self.cache.add(e)
self.cache.add(s)
for i in self.hooks:
try:
i.add(e)
except:
pass
precache.remove(e)
sigs.remove(s)
self.update_record(now, record)
if self.bypass:
for e in precache:
if e in self.cache.entries():
if e.is_expired(now):
for i in self.hooks:
try:
i.remove(e)
except:
pass
self.cache.remove(e)
else:
entry = self.cache.get(e)
if (entry is not None):
for i in self.hooks:
try:
i.update(e)
except:
pass
entry.reset_ttl(e)
else:
self.cache.add(e)
for i in self.hooks:
try:
i.add(e)
except:
pass
self.update_record(now, record) |
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Sends an outgoing packet.
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Description:
def send(self, out, addr=_MDNS_ADDR, port=_MDNS_PORT):
"""Sends an outgoing packet.""" |
# This is a quick test to see if we can parse the packets we generate
#temp = DNSIncoming(out.packet())
for i in self.intf.values():
try:
return i.sendto(out.packet(), 0, (addr, port))
except:
traceback.print_exc()
# Ignore this, it may be a temporary loss of network connection
return -1 |
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Ends the background threads, and prevent this instance from
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Description:
def close(self):
"""Ends the background threads, and prevent this instance from
servicing further queries.""" |
if globals()['_GLOBAL_DONE'] == 0:
globals()['_GLOBAL_DONE'] = 1
self.notify_all()
self.engine.notify()
self.unregister_all_services()
for i in self.intf.values():
try:
# there are cases, when we start mDNS without network
i.setsockopt(socket.SOL_IP, socket.IP_DROP_MEMBERSHIP,
socket.inet_aton(_MDNS_ADDR) + \
socket.inet_aton('0.0.0.0'))
except:
pass
i.close() |
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Executes Blurr BTS with the given records. old_state_rdd can be provided to load an older
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Description:
def execute(self, identity_records: 'RDD', old_state_rdd: Optional['RDD'] = None) -> 'RDD':
"""
Executes Blurr BTS with the given records. old_state_rdd can be provided to load an older
state from a previous run.
:param identity_records: RDD of the form Tuple[Identity, List[TimeAndRecord]]
:param old_state_rdd: A previous streaming BTS state RDD as Tuple[Identity, Streaming BTS
State]
:return: RDD[Identity, Tuple[Streaming BTS State, List of Window BTS output]]
""" |
identity_records_with_state = identity_records
if old_state_rdd:
identity_records_with_state = identity_records.fullOuterJoin(old_state_rdd)
return identity_records_with_state.map(lambda x: self._execute_per_identity_records(x)) |
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Reads the data from the given json_files path and converts them into the `Record`s format for
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Description:
def get_record_rdd_from_json_files(self,
json_files: List[str],
data_processor: DataProcessor = SimpleJsonDataProcessor(),
spark_session: Optional['SparkSession'] = None) -> 'RDD':
"""
Reads the data from the given json_files path and converts them into the `Record`s format for
processing. `data_processor` is used to process the per event data in those files to convert
them into `Record`.
:param json_files: List of json file paths. Regular Spark path wildcards are accepted.
:param data_processor: `DataProcessor` to process each event in the json files.
:param spark_session: `SparkSession` to use for execution. If None is provided then a basic
`SparkSession` is created.
:return: RDD containing Tuple[Identity, List[TimeAndRecord]] which can be used in
`execute()`
""" |
spark_context = get_spark_session(spark_session).sparkContext
raw_records: 'RDD' = spark_context.union(
[spark_context.textFile(file) for file in json_files])
return raw_records.mapPartitions(
lambda x: self.get_per_identity_records(x, data_processor)).groupByKey().mapValues(list) |
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Converts a RDD of raw events into the `Record`s format for processing. `data_processor` is
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Description:
def get_record_rdd_from_rdd(
self,
rdd: 'RDD',
data_processor: DataProcessor = SimpleDictionaryDataProcessor(),
) -> 'RDD':
"""
Converts a RDD of raw events into the `Record`s format for processing. `data_processor` is
used to process the per row data to convert them into `Record`.
:param rdd: RDD containing the raw events.
:param data_processor: `DataProcessor` to process each row in the given `rdd`.
:return: RDD containing Tuple[Identity, List[TimeAndRecord]] which can be used in
`execute()`
""" |
return rdd.mapPartitions(
lambda x: self.get_per_identity_records(x, data_processor)).groupByKey().mapValues(list) |
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Basic helper function to persist data to disk.
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Description:
def write_output_file(self,
path: str,
per_identity_data: 'RDD',
spark_session: Optional['SparkSession'] = None) -> None:
"""
Basic helper function to persist data to disk.
If window BTS was provided then the window BTS output to written in csv format, otherwise,
the streaming BTS output is written in JSON format to the `path` provided
:param path: Path where the output should be written.
:param per_identity_data: Output of the `execute()` call.
:param spark_session: `SparkSession` to use for execution. If None is provided then a basic
`SparkSession` is created.
:return:
""" |
_spark_session_ = get_spark_session(spark_session)
if not self._window_bts:
per_identity_data.flatMap(
lambda x: [json.dumps(data, cls=BlurrJSONEncoder) for data in x[1][0].items()]
).saveAsTextFile(path)
else:
# Convert to a DataFrame first so that the data can be saved as a CSV
_spark_session_.createDataFrame(per_identity_data.flatMap(lambda x: x[1][1])).write.csv(
path, header=True) |
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Basic helper function to write data to stdout. If window BTS was provided then the window
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Description:
def print_output(self, per_identity_data: 'RDD') -> None:
"""
Basic helper function to write data to stdout. If window BTS was provided then the window
BTS output is written, otherwise, the streaming BTS output is written to stdout.
WARNING - For large datasets this will be extremely slow.
:param per_identity_data: Output of the `execute()` call.
""" |
if not self._window_bts:
data = per_identity_data.flatMap(
lambda x: [json.dumps(data, cls=BlurrJSONEncoder) for data in x[1][0].items()])
else:
# Convert to a DataFrame first so that the data can be saved as a CSV
data = per_identity_data.map(
lambda x: json.dumps((x[0], x[1][1]), cls=BlurrJSONEncoder))
for row in data.collect():
print(row) |
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As distutils.spawn.find_executable, but on Windows, look up
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Description:
def find_executable(executable, path=None):
"""
As distutils.spawn.find_executable, but on Windows, look up
every extension declared in PATHEXT instead of just `.exe`
""" |
if sys.platform != 'win32':
return distutils.spawn.find_executable(executable, path)
if path is None:
path = os.environ['PATH']
paths = path.split(os.pathsep)
extensions = os.environ.get('PATHEXT', '.exe').split(os.pathsep)
base, ext = os.path.splitext(executable)
if not os.path.isfile(executable):
for p in paths:
for ext in extensions:
f = os.path.join(p, base + ext)
if os.path.isfile(f):
return f
return None
else:
return executable |
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Create and return a copy of os.environ with the specified overrides
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Description:
def create_environment_dict(overrides):
"""
Create and return a copy of os.environ with the specified overrides
""" |
result = os.environ.copy()
result.update(overrides or {})
return result |
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Retrieve credentials for `server`. If no credentials are found,
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Description:
def get(self, server):
""" Retrieve credentials for `server`. If no credentials are found,
a `StoreError` will be raised.
""" |
if not isinstance(server, six.binary_type):
server = server.encode('utf-8')
data = self._execute('get', server)
result = json.loads(data.decode('utf-8'))
# docker-credential-pass will return an object for inexistent servers
# whereas other helpers will exit with returncode != 0. For
# consistency, if no significant data is returned,
# raise CredentialsNotFound
if result['Username'] == '' and result['Secret'] == '':
raise errors.CredentialsNotFound(
'No matching credentials in {}'.format(self.program)
)
return result |
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Store credentials for `server`. Raises a `StoreError` if an error
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Description:
def store(self, server, username, secret):
""" Store credentials for `server`. Raises a `StoreError` if an error
occurs.
""" |
data_input = json.dumps({
'ServerURL': server,
'Username': username,
'Secret': secret
}).encode('utf-8')
return self._execute('store', data_input) |
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Erase credentials for `server`. Raises a `StoreError` if an error
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Description:
def erase(self, server):
""" Erase credentials for `server`. Raises a `StoreError` if an error
occurs.
""" |
if not isinstance(server, six.binary_type):
server = server.encode('utf-8')
self._execute('erase', server) |
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Injects the identity field
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Description:
def extend_schema_spec(self) -> None:
""" Injects the identity field """ |
super().extend_schema_spec()
identity_field = {
'Name': '_identity',
'Type': BtsType.STRING,
'Value': 'identity',
ATTRIBUTE_INTERNAL: True
}
if self.ATTRIBUTE_FIELDS in self._spec:
self._spec[self.ATTRIBUTE_FIELDS].insert(0, identity_field)
self.schema_loader.add_schema_spec(identity_field, self.fully_qualified_name) |
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Persists the current data group
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Description:
def _persist(self) -> None:
"""
Persists the current data group
""" |
if self._store:
self._store.save(self._key, self._snapshot) |
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Adds errors to the error store for the schema
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Description:
def add_errors(self, *errors: Union[BaseSchemaError, SchemaErrorCollection]) -> None:
""" Adds errors to the error store for the schema """ |
for error in errors:
self._error_cache.add(error) |
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Adds a key and value to the global dictionary
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Description:
def global_add(self, key: str, value: Any) -> None:
"""
Adds a key and value to the global dictionary
""" |
self.global_context[key] = value |
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Copy all the files in source directory to target.
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Description:
def _copy_files(source, target):
"""
Copy all the files in source directory to target.
Ignores subdirectories.
""" |
source_files = listdir(source)
if not exists(target):
makedirs(target)
for filename in source_files:
full_filename = join(source, filename)
if isfile(full_filename):
shutil.copy(full_filename, target) |
<SYSTEM_TASK:>
Initialises a temporary directory structure and copy of MAGICC
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Description:
def create_copy(self):
"""
Initialises a temporary directory structure and copy of MAGICC
configuration files and binary.
""" |
if self.executable is None or not isfile(self.executable):
raise FileNotFoundError(
"Could not find MAGICC{} executable: {}".format(
self.version, self.executable
)
)
if self.is_temp:
assert (
self.root_dir is None
), "A temp copy for this instance has already been created"
self.root_dir = mkdtemp(prefix="pymagicc-")
if exists(self.run_dir):
raise Exception("A copy of MAGICC has already been created.")
if not exists(self.root_dir):
makedirs(self.root_dir)
exec_dir = basename(self.original_dir)
# Copy a subset of folders from the MAGICC `original_dir`
# Also copy anything which is in the root of the MAGICC distribution
# Assumes that the MAGICC binary is in a folder one level below the root
# of the MAGICC distribution. i.e. /run/magicc.exe or /bin/magicc
dirs_to_copy = [".", "bin", "run"]
# Check that the executable is in a valid sub directory
assert exec_dir in dirs_to_copy, "binary must be in bin/ or run/ directory"
for d in dirs_to_copy:
source_dir = abspath(join(self.original_dir, "..", d))
if exists(source_dir):
_copy_files(source_dir, join(self.root_dir, d))
# Create an empty out dir
# MAGICC assumes that the 'out' directory already exists
makedirs(join(self.root_dir, "out"))
# Create basic configuration files so magicc can run
self.set_years()
self.set_config() |
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Run MAGICC and parse the output.
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Description:
def run(self, scenario=None, only=None, **kwargs):
"""
Run MAGICC and parse the output.
As a reminder, putting ``out_parameters=1`` will cause MAGICC to write out its
parameters into ``out/PARAMETERS.OUT`` and they will then be read into
``output.metadata["parameters"]`` where ``output`` is the returned object.
Parameters
----------
scenario : :obj:`pymagicc.io.MAGICCData`
Scenario to run. If None MAGICC will simply run with whatever config has
already been set.
only : list of str
If not None, only extract variables in this list.
kwargs
Other config values to pass to MAGICC for the run
Returns
-------
:obj:`pymagicc.io.MAGICCData`
MAGICCData object containing that data in its ``df`` attribute and
metadata and parameters (depending on the value of ``include_parameters``)
in its ``metadata`` attribute.
Raises
------
ValueError
If no output is found which matches the list specified in ``only``.
""" |
if not exists(self.root_dir):
raise FileNotFoundError(self.root_dir)
if self.executable is None:
raise ValueError(
"MAGICC executable not found, try setting an environment variable `MAGICC_EXECUTABLE_{}=/path/to/binary`".format(
self.version
)
)
if scenario is not None:
kwargs = self.set_emission_scenario_setup(scenario, kwargs)
yr_config = {}
if "startyear" in kwargs:
yr_config["startyear"] = kwargs.pop("startyear")
if "endyear" in kwargs:
yr_config["endyear"] = kwargs.pop("endyear")
if yr_config:
self.set_years(**yr_config)
# should be able to do some other nice metadata stuff re how magicc was run
# etc. here
kwargs.setdefault("rundate", get_date_time_string())
self.update_config(**kwargs)
self.check_config()
exec_dir = basename(self.original_dir)
command = [join(self.root_dir, exec_dir, self.binary_name)]
if not IS_WINDOWS and self.binary_name.endswith(".exe"): # pragma: no cover
command.insert(0, "wine")
# On Windows shell=True is required.
subprocess.check_call(command, cwd=self.run_dir, shell=IS_WINDOWS)
outfiles = self._get_output_filenames()
read_cols = {"climate_model": ["MAGICC{}".format(self.version)]}
if scenario is not None:
read_cols["model"] = scenario["model"].unique().tolist()
read_cols["scenario"] = scenario["scenario"].unique().tolist()
else:
read_cols.setdefault("model", ["unspecified"])
read_cols.setdefault("scenario", ["unspecified"])
mdata = None
for filepath in outfiles:
try:
openscm_var = _get_openscm_var_from_filepath(filepath)
if only is None or openscm_var in only:
tempdata = MAGICCData(
join(self.out_dir, filepath), columns=deepcopy(read_cols)
)
mdata = mdata.append(tempdata) if mdata is not None else tempdata
except (NoReaderWriterError, InvalidTemporalResError):
continue
if mdata is None:
error_msg = "No output found for only={}".format(only)
raise ValueError(error_msg)
try:
run_paras = self.read_parameters()
self.config = run_paras
mdata.metadata["parameters"] = run_paras
except FileNotFoundError:
pass
return mdata |
<SYSTEM_TASK:>
Check that our MAGICC ``.CFG`` files are set to safely work with PYMAGICC
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Description:
def check_config(self):
"""Check that our MAGICC ``.CFG`` files are set to safely work with PYMAGICC
For further detail about why this is required, please see :ref:`MAGICC flags`.
Raises
------
ValueError
If we are not certain that the config written by PYMAGICC will overwrite
all other config i.e. that there will be no unexpected behaviour. A
ValueError will also be raised if the user tries to use more than one
scenario file.
""" |
cfg_error_msg = (
"PYMAGICC is not the only tuning model that will be used by "
"`MAGCFG_USER.CFG`: your run is likely to fail/do odd things"
)
emisscen_error_msg = (
"You have more than one `FILE_EMISSCEN_X` flag set. Using more than "
"one emissions scenario is hard to debug and unnecessary with "
"Pymagicc's dataframe scenario input. Please combine all your "
"scenarios into one dataframe with Pymagicc and pandas, then feed "
"this single Dataframe into Pymagicc's run API."
)
nml_to_check = "nml_allcfgs"
usr_cfg = read_cfg_file(join(self.run_dir, "MAGCFG_USER.CFG"))
for k in usr_cfg[nml_to_check]:
if k.startswith("file_tuningmodel"):
first_tuningmodel = k in ["file_tuningmodel", "file_tuningmodel_1"]
if first_tuningmodel:
if usr_cfg[nml_to_check][k] != "PYMAGICC":
raise ValueError(cfg_error_msg)
elif usr_cfg[nml_to_check][k] not in ["USER", ""]:
raise ValueError(cfg_error_msg)
elif k.startswith("file_emisscen_"):
if usr_cfg[nml_to_check][k] not in ["NONE", ""]:
raise ValueError(emisscen_error_msg) |
<SYSTEM_TASK:>
Write an input file to disk
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Description:
def write(self, mdata, name):
"""Write an input file to disk
Parameters
----------
mdata : :obj:`pymagicc.io.MAGICCData`
A MAGICCData instance with the data to write
name : str
The name of the file to write. The file will be written to the MAGICC
instance's run directory i.e. ``self.run_dir``
""" |
mdata.write(join(self.run_dir, name), self.version) |
<SYSTEM_TASK:>
Read a parameters.out file
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<USER_TASK:>
Description:
def read_parameters(self):
"""
Read a parameters.out file
Returns
-------
dict
A dictionary containing all the configuration used by MAGICC
""" |
param_fname = join(self.out_dir, "PARAMETERS.OUT")
if not exists(param_fname):
raise FileNotFoundError("No PARAMETERS.OUT found")
with open(param_fname) as nml_file:
parameters = dict(f90nml.read(nml_file))
for group in ["nml_years", "nml_allcfgs", "nml_outputcfgs"]:
parameters[group] = dict(parameters[group])
for k, v in parameters[group].items():
parameters[group][k] = _clean_value(v)
parameters[group.replace("nml_", "")] = parameters.pop(group)
self.config = parameters
return parameters |
<SYSTEM_TASK:>
Removes a temporary copy of the MAGICC version shipped with Pymagicc.
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<USER_TASK:>
Description:
def remove_temp_copy(self):
"""
Removes a temporary copy of the MAGICC version shipped with Pymagicc.
""" |
if self.is_temp and self.root_dir is not None:
shutil.rmtree(self.root_dir)
self.root_dir = None |
<SYSTEM_TASK:>
Create a configuration file for MAGICC.
<END_TASK>
<USER_TASK:>
Description:
def set_config(
self, filename="MAGTUNE_PYMAGICC.CFG", top_level_key="nml_allcfgs", **kwargs
):
"""
Create a configuration file for MAGICC.
Writes a fortran namelist in run_dir.
Parameters
----------
filename : str
Name of configuration file to write
top_level_key : str
Name of namelist to be written in the
configuration file
kwargs
Other parameters to pass to the configuration file. No
validation on the parameters is performed.
Returns
-------
dict
The contents of the namelist which was written to file
""" |
kwargs = self._format_config(kwargs)
fname = join(self.run_dir, filename)
conf = {top_level_key: kwargs}
f90nml.write(conf, fname, force=True)
return conf |
<SYSTEM_TASK:>
Updates a configuration file for MAGICC
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<USER_TASK:>
Description:
def update_config(
self, filename="MAGTUNE_PYMAGICC.CFG", top_level_key="nml_allcfgs", **kwargs
):
"""Updates a configuration file for MAGICC
Updates the contents of a fortran namelist in the run directory,
creating a new namelist if none exists.
Parameters
----------
filename : str
Name of configuration file to write
top_level_key : str
Name of namelist to be written in the
configuration file
kwargs
Other parameters to pass to the configuration file. No
validation on the parameters is performed.
Returns
-------
dict
The contents of the namelist which was written to file
""" |
kwargs = self._format_config(kwargs)
fname = join(self.run_dir, filename)
if exists(fname):
conf = f90nml.read(fname)
else:
conf = {top_level_key: {}}
conf[top_level_key].update(kwargs)
f90nml.write(conf, fname, force=True)
return conf |
<SYSTEM_TASK:>
Set config such that radiative forcing and temperature output will be zero
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Description:
def set_zero_config(self):
"""Set config such that radiative forcing and temperature output will be zero
This method is intended as a convenience only, it does not handle everything in
an obvious way. Adjusting the parameter settings still requires great care and
may behave unepexctedly.
""" |
# zero_emissions is imported from scenarios module
zero_emissions.write(join(self.run_dir, self._scen_file_name), self.version)
time = zero_emissions.filter(variable="Emissions|CH4", region="World")[
"time"
].values
no_timesteps = len(time)
# value doesn't actually matter as calculations are done from difference but
# chose sensible value nonetheless
ch4_conc_pi = 722
ch4_conc = ch4_conc_pi * np.ones(no_timesteps)
ch4_conc_df = pd.DataFrame(
{
"time": time,
"scenario": "idealised",
"model": "unspecified",
"climate_model": "unspecified",
"variable": "Atmospheric Concentrations|CH4",
"unit": "ppb",
"todo": "SET",
"region": "World",
"value": ch4_conc,
}
)
ch4_conc_writer = MAGICCData(ch4_conc_df)
ch4_conc_filename = "HIST_CONSTANT_CH4_CONC.IN"
ch4_conc_writer.metadata = {
"header": "Constant pre-industrial CH4 concentrations"
}
ch4_conc_writer.write(join(self.run_dir, ch4_conc_filename), self.version)
fgas_conc_pi = 0
fgas_conc = fgas_conc_pi * np.ones(no_timesteps)
# MAGICC6 doesn't read this so not a problem, for MAGICC7 we might have to
# write each file separately
varname = "FGAS_CONC"
fgas_conc_df = pd.DataFrame(
{
"time": time,
"scenario": "idealised",
"model": "unspecified",
"climate_model": "unspecified",
"variable": varname,
"unit": "ppt",
"todo": "SET",
"region": "World",
"value": fgas_conc,
}
)
fgas_conc_writer = MAGICCData(fgas_conc_df)
fgas_conc_filename = "HIST_ZERO_{}.IN".format(varname)
fgas_conc_writer.metadata = {"header": "Zero concentrations"}
fgas_conc_writer.write(join(self.run_dir, fgas_conc_filename), self.version)
emis_config = self._fix_any_backwards_emissions_scen_key_in_config(
{"file_emissionscenario": self._scen_file_name}
)
self.set_config(
**emis_config,
rf_initialization_method="ZEROSTARTSHIFT",
rf_total_constantafteryr=10000,
file_co2i_emis="",
file_co2b_emis="",
co2_switchfromconc2emis_year=1750,
file_ch4i_emis="",
file_ch4b_emis="",
file_ch4n_emis="",
file_ch4_conc=ch4_conc_filename,
ch4_switchfromconc2emis_year=10000,
file_n2oi_emis="",
file_n2ob_emis="",
file_n2on_emis="",
file_n2o_conc="",
n2o_switchfromconc2emis_year=1750,
file_noxi_emis="",
file_noxb_emis="",
file_noxi_ot="",
file_noxb_ot="",
file_noxt_rf="",
file_soxnb_ot="",
file_soxi_ot="",
file_soxt_rf="",
file_soxi_emis="",
file_soxb_emis="",
file_soxn_emis="",
file_oci_emis="",
file_ocb_emis="",
file_oci_ot="",
file_ocb_ot="",
file_oci_rf="",
file_ocb_rf="",
file_bci_emis="",
file_bcb_emis="",
file_bci_ot="",
file_bcb_ot="",
file_bci_rf="",
file_bcb_rf="",
bcoc_switchfromrf2emis_year=1750,
file_nh3i_emis="",
file_nh3b_emis="",
file_nmvoci_emis="",
file_nmvocb_emis="",
file_coi_emis="",
file_cob_emis="",
file_mineraldust_rf="",
file_landuse_rf="",
file_bcsnow_rf="",
# rf_fgassum_scale=0, # this appears to do nothing, hence the next two lines
file_fgas_conc=[fgas_conc_filename] * 12,
fgas_switchfromconc2emis_year=10000,
rf_mhalosum_scale=0,
mhalo_switch_conc2emis_yr=1750,
stratoz_o3scale=0,
rf_volcanic_scale=0,
rf_solar_scale=0,
) |
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Set the start and end dates of the simulations.
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Description:
def set_years(self, startyear=1765, endyear=2100):
"""
Set the start and end dates of the simulations.
Parameters
----------
startyear : int
Start year of the simulation
endyear : int
End year of the simulation
Returns
-------
dict
The contents of the namelist
""" |
# TODO: test altering stepsperyear, I think 1, 2 and 24 should all work
return self.set_config(
"MAGCFG_NMLYEARS.CFG",
"nml_years",
endyear=endyear,
startyear=startyear,
stepsperyear=12,
) |
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Set the output configuration, minimising output as much as possible
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Description:
def set_output_variables(self, write_ascii=True, write_binary=False, **kwargs):
"""Set the output configuration, minimising output as much as possible
There are a number of configuration parameters which control which variables
are written to file and in which format. Limiting the variables that are
written to file can greatly speed up the running of MAGICC. By default,
calling this function without specifying any variables will disable all output
by setting all of MAGICC's ``out_xx`` flags to ``0``.
This convenience function should not be confused with ``set_config`` or
``update_config`` which allow the user to set/update the configuration flags
directly, without the more convenient syntax and default behaviour provided by
this function.
Parameters
----------
write_ascii : bool
If true, MAGICC is configured to write output files as human readable ascii files.
write_binary : bool
If true, MAGICC is configured to write binary output files. These files are much faster
to process and write, but are not human readable.
**kwargs:
List of variables to write out. A list of possible options are as follows. This
may not be a complete list.
'emissions',
'gwpemissions',
'sum_gwpemissions',
'concentrations',
'carboncycle',
'forcing',
'surfaceforcing',
'permafrost',
'temperature',
'sealevel',
'parameters',
'misc',
'lifetimes',
'timeseriesmix',
'rcpdata',
'summaryidx',
'inverseemis',
'tempoceanlayers',
'oceanarea',
'heatuptake',
'warnings',
'precipinput',
'aogcmtuning',
'ccycletuning',
'observationaltuning',
'keydata_1',
'keydata_2'
""" |
assert (
write_ascii or write_binary
), "write_binary and/or write_ascii must be configured"
if write_binary and write_ascii:
ascii_binary = "BOTH"
elif write_ascii:
ascii_binary = "ASCII"
else:
ascii_binary = "BINARY"
# defaults
outconfig = {
"out_emissions": 0,
"out_gwpemissions": 0,
"out_sum_gwpemissions": 0,
"out_concentrations": 0,
"out_carboncycle": 0,
"out_forcing": 0,
"out_surfaceforcing": 0,
"out_permafrost": 0,
"out_temperature": 0,
"out_sealevel": 0,
"out_parameters": 0,
"out_misc": 0,
"out_timeseriesmix": 0,
"out_rcpdata": 0,
"out_summaryidx": 0,
"out_inverseemis": 0,
"out_tempoceanlayers": 0,
"out_heatuptake": 0,
"out_ascii_binary": ascii_binary,
"out_warnings": 0,
"out_precipinput": 0,
"out_aogcmtuning": 0,
"out_ccycletuning": 0,
"out_observationaltuning": 0,
"out_keydata_1": 0,
"out_keydata_2": 0,
}
if self.version == 7:
outconfig["out_oceanarea"] = 0
outconfig["out_lifetimes"] = 0
for kw in kwargs:
val = 1 if kwargs[kw] else 0 # convert values to 0/1 instead of booleans
outconfig["out_" + kw.lower()] = val
self.update_config(**outconfig) |
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Diagnose TCR and ECS
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Description:
def diagnose_tcr_ecs(self, **kwargs):
"""Diagnose TCR and ECS
The transient climate response (TCR), is the global-mean temperature response
at time at which atmopsheric |CO2| concentrations double in a scenario where
atmospheric |CO2| concentrations are increased at 1% per year from
pre-industrial levels.
The equilibrium climate sensitivity (ECS), is the equilibrium global-mean
temperature response to an instantaneous doubling of atmospheric |CO2|
concentrations.
As MAGICC has no hysteresis in its equilibrium response to radiative forcing,
we can diagnose TCR and ECS with one experiment. However, please note that
sometimes the run length won't be long enough to allow MAGICC's oceans to
fully equilibrate and hence the ECS value might not be what you expect (it
should match the value of ``core_climatesensitivity``).
Parameters
----------
**kwargs
parameter values to use in the diagnosis e.g. ``core_climatesensitivity=4``
Returns
-------
dict
Dictionary with keys: "ecs" - the diagnosed ECS; "tcr" - the diagnosed
TCR; "timeseries" - the relevant model input and output timeseries used in
the experiment i.e. atmospheric |CO2| concentrations, total radiative
forcing and global-mean surface temperature
""" |
if self.version == 7:
raise NotImplementedError("MAGICC7 cannot yet diagnose ECS and TCR")
self._diagnose_tcr_ecs_config_setup(**kwargs)
timeseries = self.run(
scenario=None,
only=[
"Atmospheric Concentrations|CO2",
"Radiative Forcing",
"Surface Temperature",
],
)
tcr, ecs = self._get_tcr_ecs_from_diagnosis_results(timeseries)
return {"tcr": tcr, "ecs": ecs, "timeseries": timeseries} |
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Set the emissions flags correctly.
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Description:
def set_emission_scenario_setup(self, scenario, config_dict):
"""Set the emissions flags correctly.
Parameters
----------
scenario : :obj:`pymagicc.io.MAGICCData`
Scenario to run.
config_dict : dict
Dictionary with current input configurations which is to be validated and
updated where necessary.
Returns
-------
dict
Updated configuration
""" |
self.write(scenario, self._scen_file_name)
# can be lazy in this line as fix backwards key handles errors for us
config_dict["file_emissionscenario"] = self._scen_file_name
config_dict = self._fix_any_backwards_emissions_scen_key_in_config(config_dict)
return config_dict |
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Checks if a type is defined
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Description:
def contains(value: Union[str, 'Type']) -> bool:
""" Checks if a type is defined """ |
if isinstance(value, str):
return any(value.lower() == i.value for i in Type)
return any(value == i for i in Type) |
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Return the required indexes based on the given lambda function
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Description:
def _calcidxs(func):
"""Return the required indexes based on the given lambda function
and the |Timegrids| object handled by module |pub|. Raise a
|RuntimeError| if the latter is not available.
""" |
timegrids = hydpy.pub.get('timegrids')
if timegrids is None:
raise RuntimeError(
'An Indexer object has been asked for an %s array. Such an '
'array has neither been determined yet nor can it be '
'determined automatically at the moment. Either define an '
'%s array manually and pass it to the Indexer object, or make '
'a proper Timegrids object available within the pub module. '
'In usual HydPy applications, the latter is done '
'automatically.'
% (func.__name__, func.__name__))
idxs = numpy.empty(len(timegrids.init), dtype=int)
for jdx, date in enumerate(hydpy.pub.timegrids.init):
idxs[jdx] = func(date)
return idxs |
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Add the given getter function and its docstring to the
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Description:
def getter_(self, fget) -> 'BaseProperty':
"""Add the given getter function and its docstring to the
property and return it.""" |
self.fget = fget
self.set_doc(fget.__doc__)
return self |
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Return |True| or |False| to indicate if the protected
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Description:
def isready(self, obj) -> bool:
"""Return |True| or |False| to indicate if the protected
property is ready for the given object. If the object is
unknow, |ProtectedProperty| returns |False|.""" |
return vars(obj).get(self.name, False) |
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Return |True| or |False| to indicate whether all protected
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Description:
def allready(self, obj) -> bool:
"""Return |True| or |False| to indicate whether all protected
properties are ready or not.""" |
for prop in self.__properties:
if not prop.isready(obj):
return False
return True |
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Return the predefined custom value when available, otherwise,
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Description:
def call_fget(self, obj) -> Any:
"""Return the predefined custom value when available, otherwise,
the value defined by the getter function.""" |
custom = vars(obj).get(self.name)
if custom is None:
return self.fget(obj)
return custom |
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Store the given custom value and call the setter function.
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Description:
def call_fset(self, obj, value) -> None:
"""Store the given custom value and call the setter function.""" |
vars(obj)[self.name] = self.fset(obj, value) |
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Remove the predefined custom value and call the delete function.
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Description:
def call_fdel(self, obj) -> None:
"""Remove the predefined custom value and call the delete function.""" |
self.fdel(obj)
try:
del vars(obj)[self.name]
except KeyError:
pass |
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Return autodoc commands for a basemodels docstring.
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Description:
def _add_lines(specification, module):
"""Return autodoc commands for a basemodels docstring.
Note that `collection classes` (e.g. `Model`, `ControlParameters`,
`InputSequences` are placed on top of the respective section and the
`contained classes` (e.g. model methods, `ControlParameter` instances,
`InputSequence` instances at the bottom. This differs from the order
of their definition in the respective modules, but results in a better
documentation structure.
""" |
caption = _all_spec2capt.get(specification, 'dummy')
if caption.split()[-1] in ('parameters', 'sequences', 'Masks'):
exists_collectionclass = True
name_collectionclass = caption.title().replace(' ', '')
else:
exists_collectionclass = False
lines = []
if specification == 'model':
lines += [f'',
f'.. autoclass:: {module.__name__}.Model',
f' :members:',
f' :show-inheritance:',
f' :exclude-members: {", ".join(EXCLUDE_MEMBERS)}']
elif exists_collectionclass:
lines += [f'',
f'.. autoclass:: {module.__name__}.{name_collectionclass}',
f' :members:',
f' :show-inheritance:',
f' :exclude-members: {", ".join(EXCLUDE_MEMBERS)}']
lines += ['',
'.. automodule:: ' + module.__name__,
' :members:',
' :show-inheritance:']
if specification == 'model':
lines += [' :exclude-members: Model']
elif exists_collectionclass:
lines += [' :exclude-members: ' + name_collectionclass]
return lines |
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Add an exhaustive docstring to the given module of a basemodel.
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Description:
def autodoc_basemodel(module):
"""Add an exhaustive docstring to the given module of a basemodel.
Works onlye when all modules of the basemodel are named in the
standard way, e.g. `lland_model`, `lland_control`, `lland_inputs`.
""" |
autodoc_tuple2doc(module)
namespace = module.__dict__
doc = namespace.get('__doc__')
if doc is None:
doc = ''
basemodulename = namespace['__name__'].split('.')[-1]
modules = {key: value for key, value in namespace.items()
if (isinstance(value, types.ModuleType) and
key.startswith(basemodulename+'_'))}
substituter = Substituter(hydpy.substituter)
lines = []
specification = 'model'
modulename = basemodulename+'_'+specification
if modulename in modules:
module = modules[modulename]
lines += _add_title('Model features', '-')
lines += _add_lines(specification, module)
substituter.add_module(module)
for (title, spec2capt) in (('Parameter features', _PAR_SPEC2CAPT),
('Sequence features', _SEQ_SPEC2CAPT),
('Auxiliary features', _AUX_SPEC2CAPT)):
found_module = False
new_lines = _add_title(title, '-')
for (specification, caption) in spec2capt.items():
modulename = basemodulename+'_'+specification
module = modules.get(modulename)
if module:
found_module = True
new_lines += _add_title(caption, '.')
new_lines += _add_lines(specification, module)
substituter.add_module(module)
if found_module:
lines += new_lines
doc += '\n'.join(lines)
namespace['__doc__'] = doc
basemodule = importlib.import_module(namespace['__name__'])
substituter.add_module(basemodule)
substituter.update_masters()
namespace['substituter'] = substituter |
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Improves the docstrings of application models when called
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Description:
def autodoc_applicationmodel(module):
"""Improves the docstrings of application models when called
at the bottom of the respective module.
|autodoc_applicationmodel| requires, similar to
|autodoc_basemodel|, that both the application model and its
base model are defined in the conventional way.
""" |
autodoc_tuple2doc(module)
name_applicationmodel = module.__name__
name_basemodel = name_applicationmodel.split('_')[0]
module_basemodel = importlib.import_module(name_basemodel)
substituter = Substituter(module_basemodel.substituter)
substituter.add_module(module)
substituter.update_masters()
module.substituter = substituter |
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Try to return the number of the first line of the definition of a
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Description:
def _number_of_line(member_tuple):
"""Try to return the number of the first line of the definition of a
member of a module.""" |
member = member_tuple[1]
try:
return member.__code__.co_firstlineno
except AttributeError:
pass
try:
return inspect.findsource(member)[1]
except BaseException:
pass
for value in vars(member).values():
try:
return value.__code__.co_firstlineno
except AttributeError:
pass
return 0 |
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Add a short summary of all implemented members to a modules docstring.
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Description:
def autodoc_module(module):
"""Add a short summary of all implemented members to a modules docstring.
""" |
doc = getattr(module, '__doc__')
if doc is None:
doc = ''
members = []
for name, member in inspect.getmembers(module):
if ((not name.startswith('_')) and
(inspect.getmodule(member) is module)):
members.append((name, member))
members = sorted(members, key=_number_of_line)
if members:
lines = ['\n\nModule :mod:`~%s` implements the following members:\n'
% module.__name__]
for (name, member) in members:
if inspect.isfunction(member):
type_ = 'func'
elif inspect.isclass(member):
type_ = 'class'
else:
type_ = 'obj'
lines.append(' * :%s:`~%s` %s'
% (type_, name, objecttools.description(member)))
doc = doc + '\n\n' + '\n'.join(lines) + '\n\n' + 80*'_'
module.__doc__ = doc |
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Return |True| if the given member should be added to the
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Description:
def consider_member(name_member, member, module, class_=None):
"""Return |True| if the given member should be added to the
substitutions. If not return |False|.
Some examples based on the site-package |numpy|:
>>> from hydpy.core.autodoctools import Substituter
>>> import numpy
A constant like |nan| should be added:
>>> Substituter.consider_member(
... 'nan', numpy.nan, numpy)
True
Members with a prefixed underscore should not be added:
>>> Substituter.consider_member(
... '_NoValue', numpy._NoValue, numpy)
False
Members that are actually imported modules should not be added:
>>> Substituter.consider_member(
... 'warnings', numpy.warnings, numpy)
False
Members that are actually defined in other modules should
not be added:
>>> numpy.Substituter = Substituter
>>> Substituter.consider_member(
... 'Substituter', numpy.Substituter, numpy)
False
>>> del numpy.Substituter
Members that are defined in submodules of a given package
(either from the standard library or from site-packages)
should be added...
>>> Substituter.consider_member(
... 'clip', numpy.clip, numpy)
True
...but not members defined in *HydPy* submodules:
>>> import hydpy
>>> Substituter.consider_member(
... 'Node', hydpy.Node, hydpy)
False
For descriptor instances (with method `__get__`) beeing members
of classes should be added:
>>> from hydpy.auxs import anntools
>>> Substituter.consider_member(
... 'shape_neurons', anntools.ANN.shape_neurons,
... anntools, anntools.ANN)
True
""" |
if name_member.startswith('_'):
return False
if inspect.ismodule(member):
return False
real_module = getattr(member, '__module__', None)
if not real_module:
return True
if real_module != module.__name__:
if class_ and hasattr(member, '__get__'):
return True
if 'hydpy' in real_module:
return False
if module.__name__ not in real_module:
return False
return True |
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Return the reStructuredText role `func`, `class`, or `const`
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Description:
def get_role(member, cython=False):
"""Return the reStructuredText role `func`, `class`, or `const`
best describing the given member.
Some examples based on the site-package |numpy|. |numpy.clip|
is a function:
>>> from hydpy.core.autodoctools import Substituter
>>> import numpy
>>> Substituter.get_role(numpy.clip)
'func'
|numpy.ndarray| is a class:
>>> Substituter.get_role(numpy.ndarray)
'class'
|numpy.ndarray.clip| is a method, for which also the `function`
role is returned:
>>> Substituter.get_role(numpy.ndarray.clip)
'func'
For everything else the `constant` role is returned:
>>> Substituter.get_role(numpy.nan)
'const'
When analysing cython extension modules, set the option `cython`
flag to |True|. |Double| is correctly identified as a class:
>>> from hydpy.cythons import pointerutils
>>> Substituter.get_role(pointerutils.Double, cython=True)
'class'
Only with the `cython` flag beeing |True|, for everything else
the `function` text role is returned (doesn't make sense here,
but the |numpy| module is not something defined in module
|pointerutils| anyway):
>>> Substituter.get_role(pointerutils.numpy, cython=True)
'func'
""" |
if inspect.isroutine(member) or isinstance(member, numpy.ufunc):
return 'func'
elif inspect.isclass(member):
return 'class'
elif cython:
return 'func'
return 'const' |
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Add the given substitutions both as a `short2long` and a
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Description:
def add_substitution(self, short, medium, long, module):
"""Add the given substitutions both as a `short2long` and a
`medium2long` mapping.
Assume `variable1` is defined in the hydpy module `module1` and the
short and medium descriptions are `var1` and `mod1.var1`:
>>> import types
>>> module1 = types.ModuleType('hydpy.module1')
>>> from hydpy.core.autodoctools import Substituter
>>> substituter = Substituter()
>>> substituter.add_substitution(
... 'var1', 'mod1.var1', 'module1.variable1', module1)
>>> print(substituter.get_commands())
.. var1 replace:: module1.variable1
.. mod1.var1 replace:: module1.variable1
Adding `variable2` of `module2` has no effect on the predefined
substitutions:
>>> module2 = types.ModuleType('hydpy.module2')
>>> substituter.add_substitution(
... 'var2', 'mod2.var2', 'module2.variable2', module2)
>>> print(substituter.get_commands())
.. var1 replace:: module1.variable1
.. var2 replace:: module2.variable2
.. mod1.var1 replace:: module1.variable1
.. mod2.var2 replace:: module2.variable2
But when adding `variable1` of `module2`, the `short2long` mapping
of `variable1` would become inconclusive, which is why the new
one (related to `module2`) is not stored and the old one (related
to `module1`) is removed:
>>> substituter.add_substitution(
... 'var1', 'mod2.var1', 'module2.variable1', module2)
>>> print(substituter.get_commands())
.. var2 replace:: module2.variable2
.. mod1.var1 replace:: module1.variable1
.. mod2.var1 replace:: module2.variable1
.. mod2.var2 replace:: module2.variable2
Adding `variable2` of `module2` accidentally again, does not
result in any undesired side-effects:
>>> substituter.add_substitution(
... 'var2', 'mod2.var2', 'module2.variable2', module2)
>>> print(substituter.get_commands())
.. var2 replace:: module2.variable2
.. mod1.var1 replace:: module1.variable1
.. mod2.var1 replace:: module2.variable1
.. mod2.var2 replace:: module2.variable2
In order to reduce the risk of name conflicts, only the
`medium2long` mapping is supported for modules not part of the
*HydPy* package:
>>> module3 = types.ModuleType('module3')
>>> substituter.add_substitution(
... 'var3', 'mod3.var3', 'module3.variable3', module3)
>>> print(substituter.get_commands())
.. var2 replace:: module2.variable2
.. mod1.var1 replace:: module1.variable1
.. mod2.var1 replace:: module2.variable1
.. mod2.var2 replace:: module2.variable2
.. mod3.var3 replace:: module3.variable3
The only exception to this rule is |builtins|, for which only
the `short2long` mapping is supported (note also, that the
module name `builtins` is removed from string `long`):
>>> import builtins
>>> substituter.add_substitution(
... 'str', 'blt.str', ':func:`~builtins.str`', builtins)
>>> print(substituter.get_commands())
.. str replace:: :func:`str`
.. var2 replace:: module2.variable2
.. mod1.var1 replace:: module1.variable1
.. mod2.var1 replace:: module2.variable1
.. mod2.var2 replace:: module2.variable2
.. mod3.var3 replace:: module3.variable3
""" |
name = module.__name__
if 'builtin' in name:
self._short2long[short] = long.split('~')[0] + long.split('.')[-1]
else:
if ('hydpy' in name) and (short not in self._blacklist):
if short in self._short2long:
if self._short2long[short] != long:
self._blacklist.add(short)
del self._short2long[short]
else:
self._short2long[short] = long
self._medium2long[medium] = long |
<SYSTEM_TASK:>
Add the given module, its members, and their submembers.
<END_TASK>
<USER_TASK:>
Description:
def add_module(self, module, cython=False):
"""Add the given module, its members, and their submembers.
The first examples are based on the site-package |numpy|: which
is passed to method |Substituter.add_module|:
>>> from hydpy.core.autodoctools import Substituter
>>> substituter = Substituter()
>>> import numpy
>>> substituter.add_module(numpy)
Firstly, the module itself is added:
>>> substituter.find('|numpy|')
|numpy| :mod:`~numpy`
Secondly, constants like |numpy.nan| are added:
>>> substituter.find('|numpy.nan|')
|numpy.nan| :const:`~numpy.nan`
Thirdly, functions like |numpy.clip| are added:
>>> substituter.find('|numpy.clip|')
|numpy.clip| :func:`~numpy.clip`
Fourthly, clases line |numpy.ndarray| are added:
>>> substituter.find('|numpy.ndarray|')
|numpy.ndarray| :class:`~numpy.ndarray`
When adding Cython modules, the `cython` flag should be set |True|:
>>> from hydpy.cythons import pointerutils
>>> substituter.add_module(pointerutils, cython=True)
>>> substituter.find('set_pointer')
|PPDouble.set_pointer| \
:func:`~hydpy.cythons.autogen.pointerutils.PPDouble.set_pointer`
|pointerutils.PPDouble.set_pointer| \
:func:`~hydpy.cythons.autogen.pointerutils.PPDouble.set_pointer`
""" |
name_module = module.__name__.split('.')[-1]
short = ('|%s|'
% name_module)
long = (':mod:`~%s`'
% module.__name__)
self._short2long[short] = long
for (name_member, member) in vars(module).items():
if self.consider_member(
name_member, member, module):
role = self.get_role(member, cython)
short = ('|%s|'
% name_member)
medium = ('|%s.%s|'
% (name_module,
name_member))
long = (':%s:`~%s.%s`'
% (role,
module.__name__,
name_member))
self.add_substitution(short, medium, long, module)
if inspect.isclass(member):
for name_submember, submember in vars(member).items():
if self.consider_member(
name_submember, submember, module, member):
role = self.get_role(submember, cython)
short = ('|%s.%s|'
% (name_member,
name_submember))
medium = ('|%s.%s.%s|'
% (name_module,
name_member,
name_submember))
long = (':%s:`~%s.%s.%s`'
% (role,
module.__name__,
name_member,
name_submember))
self.add_substitution(short, medium, long, module) |
<SYSTEM_TASK:>
Add the modules of the given package without their members.
<END_TASK>
<USER_TASK:>
Description:
def add_modules(self, package):
"""Add the modules of the given package without their members.""" |
for name in os.listdir(package.__path__[0]):
if name.startswith('_'):
continue
name = name.split('.')[0]
short = '|%s|' % name
long = ':mod:`~%s.%s`' % (package.__package__, name)
self._short2long[short] = long |
<SYSTEM_TASK:>
Update all `master` |Substituter| objects.
<END_TASK>
<USER_TASK:>
Description:
def update_masters(self):
"""Update all `master` |Substituter| objects.
If a |Substituter| object is passed to the constructor of another
|Substituter| object, they become `master` and `slave`:
>>> from hydpy.core.autodoctools import Substituter
>>> sub1 = Substituter()
>>> from hydpy.core import devicetools
>>> sub1.add_module(devicetools)
>>> sub2 = Substituter(sub1)
>>> sub3 = Substituter(sub2)
>>> sub3.master.master is sub1
True
>>> sub2 in sub1.slaves
True
During initialization, all mappings handled by the master object
are passed to its new slave:
>>> sub3.find('Node|')
|Node| :class:`~hydpy.core.devicetools.Node`
|devicetools.Node| :class:`~hydpy.core.devicetools.Node`
Updating a slave, does not affect its master directly:
>>> from hydpy.core import hydpytools
>>> sub3.add_module(hydpytools)
>>> sub3.find('HydPy|')
|HydPy| :class:`~hydpy.core.hydpytools.HydPy`
|hydpytools.HydPy| :class:`~hydpy.core.hydpytools.HydPy`
>>> sub2.find('HydPy|')
Through calling |Substituter.update_masters|, the `medium2long`
mappings are passed from the slave to its master:
>>> sub3.update_masters()
>>> sub2.find('HydPy|')
|hydpytools.HydPy| :class:`~hydpy.core.hydpytools.HydPy`
Then each master object updates its own master object also:
>>> sub1.find('HydPy|')
|hydpytools.HydPy| :class:`~hydpy.core.hydpytools.HydPy`
In reverse, subsequent updates of master objects to not affect
their slaves directly:
>>> from hydpy.core import masktools
>>> sub1.add_module(masktools)
>>> sub1.find('Masks|')
|Masks| :class:`~hydpy.core.masktools.Masks`
|masktools.Masks| :class:`~hydpy.core.masktools.Masks`
>>> sub2.find('Masks|')
Through calling |Substituter.update_slaves|, the `medium2long`
mappings are passed the master to all of its slaves:
>>> sub1.update_slaves()
>>> sub2.find('Masks|')
|masktools.Masks| :class:`~hydpy.core.masktools.Masks`
>>> sub3.find('Masks|')
|masktools.Masks| :class:`~hydpy.core.masktools.Masks`
""" |
if self.master is not None:
self.master._medium2long.update(self._medium2long)
self.master.update_masters() |
<SYSTEM_TASK:>
Return a string containing multiple `reStructuredText`
<END_TASK>
<USER_TASK:>
Description:
def get_commands(self, source=None):
"""Return a string containing multiple `reStructuredText`
replacements with the substitutions currently defined.
Some examples based on the subpackage |optiontools|:
>>> from hydpy.core.autodoctools import Substituter
>>> substituter = Substituter()
>>> from hydpy.core import optiontools
>>> substituter.add_module(optiontools)
When calling |Substituter.get_commands| with the `source`
argument, the complete `short2long` and `medium2long` mappings
are translated into replacement commands (only a few of them
are shown):
>>> print(substituter.get_commands())
.. |Options.autocompile| replace:: \
:const:`~hydpy.core.optiontools.Options.autocompile`
.. |Options.checkseries| replace:: \
:const:`~hydpy.core.optiontools.Options.checkseries`
...
.. |optiontools.Options.warntrim| replace:: \
:const:`~hydpy.core.optiontools.Options.warntrim`
.. |optiontools.Options| replace:: \
:class:`~hydpy.core.optiontools.Options`
Through passing a string (usually the source code of a file
to be documented), only the replacement commands relevant for
this string are translated:
>>> from hydpy.core import objecttools
>>> import inspect
>>> source = inspect.getsource(objecttools)
>>> print(substituter.get_commands(source))
.. |Options.reprdigits| replace:: \
:const:`~hydpy.core.optiontools.Options.reprdigits`
""" |
commands = []
for key, value in self:
if (source is None) or (key in source):
commands.append('.. %s replace:: %s' % (key, value))
return '\n'.join(commands) |
<SYSTEM_TASK:>
Print all substitutions that include the given text string.
<END_TASK>
<USER_TASK:>
Description:
def find(self, text):
"""Print all substitutions that include the given text string.""" |
for key, value in self:
if (text in key) or (text in value):
print(key, value) |
<SYSTEM_TASK:>
Add print commands time to the given function informing about
<END_TASK>
<USER_TASK:>
Description:
def print_progress(wrapped, _=None, args=None, kwargs=None):
"""Add print commands time to the given function informing about
execution time.
To show how the |print_progress| decorator works, we need to modify the
functions used by |print_progress| to gain system time information
available in module |time|.
First, we mock the functions |time.strftime| and |time.perf_counter|:
>>> import time
>>> from unittest import mock
>>> strftime = time.strftime
>>> perf_counter = time.perf_counter
>>> strftime_mock = mock.MagicMock()
>>> time.strftime = strftime_mock
>>> time.perf_counter = mock.MagicMock()
The mock of |time.strftime| shall respond to two calls, as if the first
call to a decorated function occurs at quarter past eight, and the second
one two seconds later:
>>> time.strftime.side_effect = '20:15:00', '20:15:02'
The mock of |time.perf_counter| shall respond to four calls, as if the
subsequent calls by decorated functions occur at second 1, 3, 4, and 7:
>>> time.perf_counter.side_effect = 1, 3, 4, 7
Now we decorate two test functions. The first one does nothing; the
second one only calls the first one:
>>> from hydpy.core.printtools import print_progress
>>> @print_progress
... def test1():
... pass
>>> @print_progress
... def test2():
... test1()
The first example shows that the output is appropriately indented,
tat the returned times are at the right place, that the calculated
execution the is correct, and that the mock of |time.strftime|
received a valid format string:
>>> from hydpy import pub
>>> pub.options.printprogress = True
>>> test2()
method test2 started at 20:15:00
method test1 started at 20:15:02
seconds elapsed: 1
seconds elapsed: 6
>>> strftime_mock.call_args
call('%H:%M:%S')
The second example verifies that resetting the indentation works:
>>> time.strftime.side_effect = '20:15:00', '20:15:02'
>>> time.perf_counter.side_effect = 1, 3, 4, 7
>>> test2()
method test2 started at 20:15:00
method test1 started at 20:15:02
seconds elapsed: 1
seconds elapsed: 6
The last example shows that disabling the |Options.printprogress|
option works as expected:
>>> pub.options.printprogress = False
>>> test2()
>>> time.strftime = strftime
>>> time.perf_counter = perf_counter
""" |
global _printprogress_indentation
_printprogress_indentation += 4
try:
if hydpy.pub.options.printprogress:
blanks = ' ' * _printprogress_indentation
name = wrapped.__name__
time_ = time.strftime('%H:%M:%S')
with PrintStyle(color=34, font=1):
print(f'{blanks}method {name} started at {time_}')
seconds = time.perf_counter()
sys.stdout.flush()
wrapped(*args, **kwargs)
blanks = ' ' * (_printprogress_indentation+4)
seconds = time.perf_counter()-seconds
with PrintStyle(color=34, font=1):
print(f'{blanks}seconds elapsed: {seconds}')
sys.stdout.flush()
else:
wrapped(*args, **kwargs)
finally:
_printprogress_indentation -= 4 |
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