after_merge
stringlengths 28
79.6k
| before_merge
stringlengths 20
79.6k
| url
stringlengths 38
71
| full_traceback
stringlengths 43
922k
| traceback_type
stringclasses 555
values |
|---|---|---|---|---|
def load(config_details):
"""Load the configuration from a working directory and a list of
configuration files. Files are loaded in order, and merged on top
of each other to create the final configuration.
Return a fully interpolated, extended and validated configuration.
"""
def build_service(filename, service_name, service_dict):
loader = ServiceLoader(
config_details.working_dir, filename, service_name, service_dict
)
service_dict = loader.make_service_dict()
validate_paths(service_dict)
return service_dict
def load_file(filename, config):
processed_config = interpolate_environment_variables(config)
validate_against_fields_schema(processed_config)
return [
build_service(filename, name, service_config)
for name, service_config in processed_config.items()
]
def merge_services(base, override):
all_service_names = set(base) | set(override)
return {
name: merge_service_dicts(base.get(name, {}), override.get(name, {}))
for name in all_service_names
}
config_file = config_details.config_files[0]
validate_top_level_object(config_file.config)
for next_file in config_details.config_files[1:]:
validate_top_level_object(next_file.config)
config_file = ConfigFile(
config_file.filename, merge_services(config_file.config, next_file.config)
)
return load_file(config_file.filename, config_file.config)
|
def load(config_details):
"""Load the configuration from a working directory and a list of
configuration files. Files are loaded in order, and merged on top
of each other to create the final configuration.
Return a fully interpolated, extended and validated configuration.
"""
def build_service(filename, service_name, service_dict):
loader = ServiceLoader(
config_details.working_dir, filename, service_name, service_dict
)
service_dict = loader.make_service_dict()
validate_paths(service_dict)
return service_dict
def load_file(filename, config):
processed_config = pre_process_config(config)
validate_against_fields_schema(processed_config)
return [
build_service(filename, name, service_config)
for name, service_config in processed_config.items()
]
def merge_services(base, override):
all_service_names = set(base) | set(override)
return {
name: merge_service_dicts(base.get(name, {}), override.get(name, {}))
for name in all_service_names
}
config_file = config_details.config_files[0]
for next_file in config_details.config_files[1:]:
config_file = ConfigFile(
config_file.filename, merge_services(config_file.config, next_file.config)
)
return load_file(config_file.filename, config_file.config)
|
https://github.com/docker/compose/issues/2203
|
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 53, in main
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 23, in sys_dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 26, in dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 163, in perform_command
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 54, in project_from_options
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 90, in get_project
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 215, in load
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 205, in merge_services
TypeError: 'NoneType' object is not iterable
|
TypeError
|
def load_file(filename, config):
processed_config = interpolate_environment_variables(config)
validate_against_fields_schema(processed_config)
return [
build_service(filename, name, service_config)
for name, service_config in processed_config.items()
]
|
def load_file(filename, config):
processed_config = pre_process_config(config)
validate_against_fields_schema(processed_config)
return [
build_service(filename, name, service_config)
for name, service_config in processed_config.items()
]
|
https://github.com/docker/compose/issues/2203
|
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 53, in main
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 23, in sys_dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 26, in dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 163, in perform_command
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 54, in project_from_options
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 90, in get_project
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 215, in load
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 205, in merge_services
TypeError: 'NoneType' object is not iterable
|
TypeError
|
def validate_and_construct_extends(self):
extends = self.service_dict["extends"]
if not isinstance(extends, dict):
extends = {"service": extends}
validate_extends_file_path(self.service_name, extends, self.filename)
self.extended_config_path = self.get_extended_config_path(extends)
self.extended_service_name = extends["service"]
config = load_yaml(self.extended_config_path)
validate_top_level_object(config)
full_extended_config = interpolate_environment_variables(config)
validate_extended_service_exists(
self.extended_service_name, full_extended_config, self.extended_config_path
)
validate_against_fields_schema(full_extended_config)
self.extended_config = full_extended_config[self.extended_service_name]
|
def validate_and_construct_extends(self):
extends = self.service_dict["extends"]
if not isinstance(extends, dict):
extends = {"service": extends}
validate_extends_file_path(self.service_name, extends, self.filename)
self.extended_config_path = self.get_extended_config_path(extends)
self.extended_service_name = extends["service"]
full_extended_config = pre_process_config(load_yaml(self.extended_config_path))
validate_extended_service_exists(
self.extended_service_name, full_extended_config, self.extended_config_path
)
validate_against_fields_schema(full_extended_config)
self.extended_config = full_extended_config[self.extended_service_name]
|
https://github.com/docker/compose/issues/2203
|
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 53, in main
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 23, in sys_dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 26, in dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 163, in perform_command
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 54, in project_from_options
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 90, in get_project
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 215, in load
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 205, in merge_services
TypeError: 'NoneType' object is not iterable
|
TypeError
|
def validate_service_names(config):
for service_name in config.keys():
if not isinstance(service_name, six.string_types):
raise ConfigurationError(
"Service name: {} needs to be a string, eg '{}'".format(
service_name, service_name
)
)
|
def validate_service_names(func):
@wraps(func)
def func_wrapper(config):
for service_name in config.keys():
if type(service_name) is int:
raise ConfigurationError(
"Service name: {} needs to be a string, eg '{}'".format(
service_name, service_name
)
)
return func(config)
return func_wrapper
|
https://github.com/docker/compose/issues/2203
|
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 53, in main
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 23, in sys_dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 26, in dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 163, in perform_command
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 54, in project_from_options
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 90, in get_project
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 215, in load
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 205, in merge_services
TypeError: 'NoneType' object is not iterable
|
TypeError
|
def validate_top_level_object(config):
if not isinstance(config, dict):
raise ConfigurationError(
"Top level object needs to be a dictionary. Check your .yml file "
"that you have defined a service at the top level."
)
validate_service_names(config)
|
def validate_top_level_object(func):
@wraps(func)
def func_wrapper(config):
if not isinstance(config, dict):
raise ConfigurationError(
"Top level object needs to be a dictionary. Check your .yml file that you have defined a service at the top level."
)
return func(config)
return func_wrapper
|
https://github.com/docker/compose/issues/2203
|
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 53, in main
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 23, in sys_dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 26, in dispatch
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 163, in perform_command
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 54, in project_from_options
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 90, in get_project
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 215, in load
File "/compose/build/docker-compose/out00-PYZ.pyz/compose.config.config", line 205, in merge_services
TypeError: 'NoneType' object is not iterable
|
TypeError
|
def friendly_error_message():
try:
yield
except SSLError as e:
raise errors.UserError("SSL error: %s" % e)
except ConnectionError:
if call_silently(["which", "docker"]) != 0:
if is_mac():
raise errors.DockerNotFoundMac()
elif is_ubuntu():
raise errors.DockerNotFoundUbuntu()
else:
raise errors.DockerNotFoundGeneric()
elif call_silently(["which", "docker-machine"]) == 0:
raise errors.ConnectionErrorDockerMachine()
else:
raise errors.ConnectionErrorGeneric(get_client().base_url)
|
def friendly_error_message():
try:
yield
except SSLError as e:
raise errors.UserError("SSL error: %s" % e)
except ConnectionError:
if call_silently(["which", "docker"]) != 0:
if is_mac():
raise errors.DockerNotFoundMac()
elif is_ubuntu():
raise errors.DockerNotFoundUbuntu()
else:
raise errors.DockerNotFoundGeneric()
elif call_silently(["which", "boot2docker"]) == 0:
raise errors.ConnectionErrorDockerMachine()
else:
raise errors.ConnectionErrorGeneric(self.get_client().base_url)
|
https://github.com/docker/compose/issues/2133
|
Traceback (most recent call last):
File "C:\Python27\Scripts\docker-compose-script.py", line 9, in <module>
load_entry_point('docker-compose==1.5.0.dev0', 'console_scripts', 'docker-compose')()
File "C:\Python27\lib\site-packages\compose\cli\main.py", line 51, in main
command.sys_dispatch()
File "C:\Python27\lib\site-packages\compose\cli\docopt_command.py", line 23, in sys_dispatch
self.dispatch(sys.argv[1:], None)
File "C:\Python27\lib\site-packages\compose\cli\command.py", line 46, in dispatch
raise errors.ConnectionErrorGeneric(self.get_client().base_url)
AttributeError: 'TopLevelCommand' object has no attribute 'get_client'
|
AttributeError
|
def loop(self):
self._init_readers()
while self._num_running > 0:
try:
item, exception = self.queue.get(timeout=0.1)
if exception:
raise exception
if item is STOP:
self._num_running -= 1
else:
yield item
except Empty:
pass
# See https://github.com/docker/compose/issues/189
except thread.error:
raise KeyboardInterrupt()
|
def loop(self):
self._init_readers()
while self._num_running > 0:
try:
item, exception = self.queue.get(timeout=0.1)
if exception:
raise exception
if item is STOP:
self._num_running -= 1
else:
yield item
except Empty:
pass
|
https://github.com/docker/compose/issues/189
|
^CGracefully stopping... (press Ctrl+C again to force)
Stopping dailylead_db_1...
Stopping dailylead_queue_1...
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.main", line 39, in main
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.docopt_command", line 21, in sys_dispatch
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.command", line 30, in dispatch
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.docopt_command", line 24, in dispatch
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.command", line 47, in perform_command
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.docopt_command", line 27, in perform_command
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.main", line 316, in up
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.log_printer", line 20, in run
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/fig.cli.multiplexer", line 20, in loop
File "/Users/ben/fig/build/fig/out00-PYZ.pyz/Queue", line 182, in get
thread.error: release unlocked lock
|
thread.error
|
def resolve_extends(self, service_dict):
if "extends" not in service_dict:
return service_dict
extends_options = self.validate_extends_options(
service_dict["name"], service_dict["extends"]
)
if self.working_dir is None:
raise Exception("No working_dir passed to ServiceLoader()")
if "file" in extends_options:
extends_from_filename = extends_options["file"]
other_config_path = expand_path(self.working_dir, extends_from_filename)
else:
other_config_path = self.filename
other_working_dir = os.path.dirname(other_config_path)
other_already_seen = self.already_seen + [self.signature(service_dict["name"])]
other_loader = ServiceLoader(
working_dir=other_working_dir,
filename=other_config_path,
already_seen=other_already_seen,
)
base_service = extends_options["service"]
other_config = load_yaml(other_config_path)
if base_service not in other_config:
msg = ("Cannot extend service '%s' in %s: Service not found") % (
base_service,
other_config_path,
)
raise ConfigurationError(msg)
other_service_dict = other_config[base_service]
other_loader.detect_cycle(extends_options["service"])
other_service_dict = other_loader.make_service_dict(
service_dict["name"],
other_service_dict,
)
validate_extended_service_dict(
other_service_dict,
filename=other_config_path,
service=extends_options["service"],
)
return merge_service_dicts(other_service_dict, service_dict)
|
def resolve_extends(self, service_dict):
if "extends" not in service_dict:
return service_dict
extends_options = self.validate_extends_options(
service_dict["name"], service_dict["extends"]
)
if self.working_dir is None:
raise Exception("No working_dir passed to ServiceLoader()")
if "file" in extends_options:
extends_from_filename = extends_options["file"]
other_config_path = expand_path(self.working_dir, extends_from_filename)
else:
other_config_path = self.filename
other_working_dir = os.path.dirname(other_config_path)
other_already_seen = self.already_seen + [self.signature(service_dict["name"])]
other_loader = ServiceLoader(
working_dir=other_working_dir,
filename=other_config_path,
already_seen=other_already_seen,
)
other_config = load_yaml(other_config_path)
other_service_dict = other_config[extends_options["service"]]
other_loader.detect_cycle(extends_options["service"])
other_service_dict = other_loader.make_service_dict(
service_dict["name"],
other_service_dict,
)
validate_extended_service_dict(
other_service_dict,
filename=other_config_path,
service=extends_options["service"],
)
return merge_service_dicts(other_service_dict, service_dict)
|
https://github.com/docker/compose/issues/1826
|
$ docker-compose up -d
Traceback (most recent call last):
File "/Users/aanand/.virtualenvs/docker-compose/bin/docker-compose", line 9, in <module>
load_entry_point('docker-compose==1.4.0.dev0', 'console_scripts', 'docker-compose')()
File "/Users/aanand/work/docker/compose/compose/cli/main.py", line 39, in main
command.sys_dispatch()
File "/Users/aanand/work/docker/compose/compose/cli/docopt_command.py", line 21, in sys_dispatch
self.dispatch(sys.argv[1:], None)
File "/Users/aanand/work/docker/compose/compose/cli/command.py", line 27, in dispatch
super(Command, self).dispatch(*args, **kwargs)
File "/Users/aanand/work/docker/compose/compose/cli/docopt_command.py", line 24, in dispatch
self.perform_command(*self.parse(argv, global_options))
File "/Users/aanand/work/docker/compose/compose/cli/command.py", line 57, in perform_command
verbose=options.get('--verbose'))
File "/Users/aanand/work/docker/compose/compose/cli/command.py", line 78, in get_project
config.load(config_details),
File "/Users/aanand/work/docker/compose/compose/config/config.py", line 132, in load
service_dict = loader.make_service_dict(service_name, service_dict)
File "/Users/aanand/work/docker/compose/compose/config/config.py", line 156, in make_service_dict
service_dict = self.resolve_extends(service_dict)
File "/Users/aanand/work/docker/compose/compose/config/config.py", line 183, in resolve_extends
other_service_dict = other_config[extends_options['service']]
KeyError: 'foo'
|
KeyError
|
def create_container(
self,
one_off=False,
insecure_registry=False,
do_build=True,
intermediate_container=None,
**override_options,
):
"""
Create a container for this service. If the image doesn't exist, attempt to pull
it.
"""
container_options = self._get_container_create_options(
override_options,
one_off=one_off,
intermediate_container=intermediate_container,
)
if do_build and self.can_be_built() and not self.client.images(name=self.full_name):
self.build()
try:
return Container.create(self.client, **container_options)
except APIError as e:
if (
e.response.status_code == 404
and e.explanation
and "No such image" in str(e.explanation)
):
self.pull(insecure_registry=insecure_registry)
return Container.create(self.client, **container_options)
raise
|
def create_container(
self,
one_off=False,
insecure_registry=False,
do_build=True,
intermediate_container=None,
**override_options,
):
"""
Create a container for this service. If the image doesn't exist, attempt to pull
it.
"""
container_options = self._get_container_create_options(
override_options,
one_off=one_off,
intermediate_container=intermediate_container,
)
if do_build and self.can_be_built() and not self.client.images(name=self.full_name):
self.build()
try:
return Container.create(self.client, **container_options)
except APIError as e:
if (
e.response.status_code == 404
and e.explanation
and "No such image" in str(e.explanation)
):
log.info("Pulling image %s..." % container_options["image"])
output = self.client.pull(
container_options["image"],
stream=True,
insecure_registry=insecure_registry,
)
stream_output(output, sys.stdout)
return Container.create(self.client, **container_options)
raise
|
https://github.com/docker/compose/issues/923
|
Pulling image 50ff1e85c429:latest...
Pulling repository 50ff1e85c429
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 31, in main
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 21, in sys_dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 27, in dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 24, in dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 59, in perform_command
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 445, in up
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.project", line 183, in up
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.service", line 258, in recreate_containers
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.service", line 243, in create_container
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.progress_stream", line 37, in stream_output
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.progress_stream", line 50, in print_output_event
compose.progress_stream.StreamOutputError: Error: image library/50ff1e85c429:latest not found
|
compose.progress_stream.StreamOutputError
|
def _get_container_create_options(
self, override_options, one_off=False, intermediate_container=None
):
container_options = dict(
(k, self.options[k]) for k in DOCKER_CONFIG_KEYS if k in self.options
)
container_options.update(override_options)
container_options["name"] = self._next_container_name(
self.containers(stopped=True, one_off=one_off), one_off
)
# If a qualified hostname was given, split it into an
# unqualified hostname and a domainname unless domainname
# was also given explicitly. This matches the behavior of
# the official Docker CLI in that scenario.
if (
"hostname" in container_options
and "domainname" not in container_options
and "." in container_options["hostname"]
):
parts = container_options["hostname"].partition(".")
container_options["hostname"] = parts[0]
container_options["domainname"] = parts[2]
if "ports" in container_options or "expose" in self.options:
ports = []
all_ports = container_options.get("ports", []) + self.options.get("expose", [])
for port in all_ports:
port = str(port)
if ":" in port:
port = port.split(":")[-1]
if "/" in port:
port = tuple(port.split("/"))
ports.append(port)
container_options["ports"] = ports
if "volumes" in container_options:
container_options["volumes"] = dict(
(parse_volume_spec(v).internal, {}) for v in container_options["volumes"]
)
if self.can_be_built():
container_options["image"] = self.full_name
# Delete options which are only used when starting
for key in DOCKER_START_KEYS:
container_options.pop(key, None)
container_options["host_config"] = self._get_container_host_config(
override_options, one_off=one_off, intermediate_container=intermediate_container
)
return container_options
|
def _get_container_create_options(
self, override_options, one_off=False, intermediate_container=None
):
container_options = dict(
(k, self.options[k]) for k in DOCKER_CONFIG_KEYS if k in self.options
)
container_options.update(override_options)
container_options["name"] = self._next_container_name(
self.containers(stopped=True, one_off=one_off), one_off
)
# If a qualified hostname was given, split it into an
# unqualified hostname and a domainname unless domainname
# was also given explicitly. This matches the behavior of
# the official Docker CLI in that scenario.
if (
"hostname" in container_options
and "domainname" not in container_options
and "." in container_options["hostname"]
):
parts = container_options["hostname"].partition(".")
container_options["hostname"] = parts[0]
container_options["domainname"] = parts[2]
if "ports" in container_options or "expose" in self.options:
ports = []
all_ports = container_options.get("ports", []) + self.options.get("expose", [])
for port in all_ports:
port = str(port)
if ":" in port:
port = port.split(":")[-1]
if "/" in port:
port = tuple(port.split("/"))
ports.append(port)
container_options["ports"] = ports
if "volumes" in container_options:
container_options["volumes"] = dict(
(parse_volume_spec(v).internal, {}) for v in container_options["volumes"]
)
if self.can_be_built():
container_options["image"] = self.full_name
else:
container_options["image"] = self._get_image_name(container_options["image"])
# Delete options which are only used when starting
for key in DOCKER_START_KEYS:
container_options.pop(key, None)
container_options["host_config"] = self._get_container_host_config(
override_options, one_off=one_off, intermediate_container=intermediate_container
)
return container_options
|
https://github.com/docker/compose/issues/923
|
Pulling image 50ff1e85c429:latest...
Pulling repository 50ff1e85c429
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 31, in main
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 21, in sys_dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 27, in dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 24, in dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 59, in perform_command
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 445, in up
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.project", line 183, in up
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.service", line 258, in recreate_containers
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.service", line 243, in create_container
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.progress_stream", line 37, in stream_output
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.progress_stream", line 50, in print_output_event
compose.progress_stream.StreamOutputError: Error: image library/50ff1e85c429:latest not found
|
compose.progress_stream.StreamOutputError
|
def pull(self, insecure_registry=False):
if "image" not in self.options:
return
repo, tag = parse_repository_tag(self.options["image"])
tag = tag or "latest"
log.info("Pulling %s (%s:%s)..." % (self.name, repo, tag))
output = self.client.pull(
repo, tag=tag, stream=True, insecure_registry=insecure_registry
)
stream_output(output, sys.stdout)
|
def pull(self, insecure_registry=False):
if "image" in self.options:
image_name = self._get_image_name(self.options["image"])
log.info("Pulling %s (%s)..." % (self.name, image_name))
self.client.pull(image_name, insecure_registry=insecure_registry)
|
https://github.com/docker/compose/issues/923
|
Pulling image 50ff1e85c429:latest...
Pulling repository 50ff1e85c429
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 31, in main
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 21, in sys_dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 27, in dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.docopt_command", line 24, in dispatch
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.command", line 59, in perform_command
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.cli.main", line 445, in up
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.project", line 183, in up
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.service", line 258, in recreate_containers
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.service", line 243, in create_container
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.progress_stream", line 37, in stream_output
File "/Users/ben/fig/build/docker-compose/out00-PYZ.pyz/compose.progress_stream", line 50, in print_output_event
compose.progress_stream.StreamOutputError: Error: image library/50ff1e85c429:latest not found
|
compose.progress_stream.StreamOutputError
|
def run(self, project, options):
"""
Run a one-off command on a service.
For example:
$ docker-compose run web python manage.py shell
By default, linked services will be started, unless they are already
running. If you do not want to start linked services, use
`docker-compose run --no-deps SERVICE COMMAND [ARGS...]`.
Usage: run [options] [-e KEY=VAL...] SERVICE [COMMAND] [ARGS...]
Options:
--allow-insecure-ssl Allow insecure connections to the docker
registry
-d Detached mode: Run container in the background, print
new container name.
--entrypoint CMD Override the entrypoint of the image.
-e KEY=VAL Set an environment variable (can be used multiple times)
--no-deps Don't start linked services.
--rm Remove container after run. Ignored in detached mode.
--service-ports Run command with the service's ports enabled and mapped
to the host.
-T Disable pseudo-tty allocation. By default `docker-compose run`
allocates a TTY.
"""
service = project.get_service(options["SERVICE"])
insecure_registry = options["--allow-insecure-ssl"]
if not options["--no-deps"]:
deps = service.get_linked_names()
if len(deps) > 0:
project.up(
service_names=deps,
start_links=True,
recreate=False,
insecure_registry=insecure_registry,
detach=options["-d"],
)
tty = True
if options["-d"] or options["-T"] or not sys.stdin.isatty():
tty = False
if options["COMMAND"]:
command = [options["COMMAND"]] + options["ARGS"]
else:
command = service.options.get("command")
container_options = {
"command": command,
"tty": tty,
"stdin_open": not options["-d"],
"detach": options["-d"],
}
if options["-e"]:
# Merge environment from config with -e command line
container_options["environment"] = dict(
parse_environment(service.options.get("environment")),
**parse_environment(options["-e"]),
)
if options["--entrypoint"]:
container_options["entrypoint"] = options.get("--entrypoint")
container = service.create_container(
one_off=True, insecure_registry=insecure_registry, **container_options
)
service_ports = None
if options["--service-ports"]:
service_ports = service.options["ports"]
if options["-d"]:
service.start_container(container, ports=service_ports, one_off=True)
print(container.name)
else:
service.start_container(container, ports=service_ports, one_off=True)
dockerpty.start(project.client, container.id, interactive=not options["-T"])
exit_code = container.wait()
if options["--rm"]:
log.info("Removing %s..." % container.name)
project.client.remove_container(container.id)
sys.exit(exit_code)
|
def run(self, project, options):
"""
Run a one-off command on a service.
For example:
$ docker-compose run web python manage.py shell
By default, linked services will be started, unless they are already
running. If you do not want to start linked services, use
`docker-compose run --no-deps SERVICE COMMAND [ARGS...]`.
Usage: run [options] [-e KEY=VAL...] SERVICE [COMMAND] [ARGS...]
Options:
--allow-insecure-ssl Allow insecure connections to the docker
registry
-d Detached mode: Run container in the background, print
new container name.
--entrypoint CMD Override the entrypoint of the image.
-e KEY=VAL Set an environment variable (can be used multiple times)
--no-deps Don't start linked services.
--rm Remove container after run. Ignored in detached mode.
--service-ports Run command with the service's ports enabled and mapped
to the host.
-T Disable pseudo-tty allocation. By default `docker-compose run`
allocates a TTY.
"""
service = project.get_service(options["SERVICE"])
insecure_registry = options["--allow-insecure-ssl"]
if not options["--no-deps"]:
deps = service.get_linked_names()
if len(deps) > 0:
project.up(
service_names=deps,
start_links=True,
recreate=False,
insecure_registry=insecure_registry,
detach=options["-d"],
)
tty = True
if options["-d"] or options["-T"] or not sys.stdin.isatty():
tty = False
if options["COMMAND"]:
command = [options["COMMAND"]] + options["ARGS"]
else:
command = service.options.get("command")
container_options = {
"command": command,
"tty": tty,
"stdin_open": not options["-d"],
"detach": options["-d"],
}
if options["-e"]:
for option in options["-e"]:
if "environment" not in service.options:
service.options["environment"] = {}
k, v = option.split("=", 1)
service.options["environment"][k] = v
if options["--entrypoint"]:
container_options["entrypoint"] = options.get("--entrypoint")
container = service.create_container(
one_off=True, insecure_registry=insecure_registry, **container_options
)
service_ports = None
if options["--service-ports"]:
service_ports = service.options["ports"]
if options["-d"]:
service.start_container(container, ports=service_ports, one_off=True)
print(container.name)
else:
service.start_container(container, ports=service_ports, one_off=True)
dockerpty.start(project.client, container.id, interactive=not options["-T"])
exit_code = container.wait()
if options["--rm"]:
log.info("Removing %s..." % container.name)
project.client.remove_container(container.id)
sys.exit(exit_code)
|
https://github.com/docker/compose/issues/927
|
$ fig run -e BLA=bla bliep
Traceback (most recent call last):
File "/usr/local/bin/fig", line 9, in <module>
load_entry_point('fig==1.0.1', 'console_scripts', 'fig')()
File "/usr/local/lib/python2.7/site-packages/fig/cli/main.py", line 31, in main
command.sys_dispatch()
File "/usr/local/lib/python2.7/site-packages/fig/cli/docopt_command.py", line 21, in sys_dispatch
self.dispatch(sys.argv[1:], None)
File "/usr/local/lib/python2.7/site-packages/fig/cli/command.py", line 28, in dispatch
super(Command, self).dispatch(*args, **kwargs)
File "/usr/local/lib/python2.7/site-packages/fig/cli/docopt_command.py", line 24, in dispatch
self.perform_command(*self.parse(argv, global_options))
File "/usr/local/lib/python2.7/site-packages/fig/cli/command.py", line 56, in perform_command
handler(project, command_options)
File "/usr/local/lib/python2.7/site-packages/fig/cli/main.py", line 312, in run
service.options['environment'][k] = v
TypeError: list indices must be integers, not unicode
|
TypeError
|
def _get_container_create_options(self, override_options, one_off=False):
container_options = dict(
(k, self.options[k]) for k in DOCKER_CONFIG_KEYS if k in self.options
)
container_options.update(override_options)
container_options["name"] = self._next_container_name(
self.containers(stopped=True, one_off=one_off), one_off
)
# If a qualified hostname was given, split it into an
# unqualified hostname and a domainname unless domainname
# was also given explicitly. This matches the behavior of
# the official Docker CLI in that scenario.
if (
"hostname" in container_options
and "domainname" not in container_options
and "." in container_options["hostname"]
):
parts = container_options["hostname"].partition(".")
container_options["hostname"] = parts[0]
container_options["domainname"] = parts[2]
if "ports" in container_options or "expose" in self.options:
ports = []
all_ports = container_options.get("ports", []) + self.options.get("expose", [])
for port in all_ports:
port = str(port)
if ":" in port:
port = port.split(":")[-1]
if "/" in port:
port = tuple(port.split("/"))
ports.append(port)
container_options["ports"] = ports
if "volumes" in container_options:
container_options["volumes"] = dict(
(parse_volume_spec(v).internal, {}) for v in container_options["volumes"]
)
container_options["environment"] = build_environment(container_options)
if self.can_be_built():
container_options["image"] = self.full_name
else:
container_options["image"] = self._get_image_name(container_options["image"])
# Delete options which are only used when starting
for key in DOCKER_START_KEYS:
container_options.pop(key, None)
return container_options
|
def _get_container_create_options(self, override_options, one_off=False):
container_options = dict(
(k, self.options[k]) for k in DOCKER_CONFIG_KEYS if k in self.options
)
container_options.update(override_options)
container_options["name"] = self._next_container_name(
self.containers(stopped=True, one_off=one_off), one_off
)
# If a qualified hostname was given, split it into an
# unqualified hostname and a domainname unless domainname
# was also given explicitly. This matches the behavior of
# the official Docker CLI in that scenario.
if (
"hostname" in container_options
and "domainname" not in container_options
and "." in container_options["hostname"]
):
parts = container_options["hostname"].partition(".")
container_options["hostname"] = parts[0]
container_options["domainname"] = parts[2]
if "ports" in container_options or "expose" in self.options:
ports = []
all_ports = container_options.get("ports", []) + self.options.get("expose", [])
for port in all_ports:
port = str(port)
if ":" in port:
port = port.split(":")[-1]
if "/" in port:
port = tuple(port.split("/"))
ports.append(port)
container_options["ports"] = ports
if "volumes" in container_options:
container_options["volumes"] = dict(
(parse_volume_spec(v).internal, {}) for v in container_options["volumes"]
)
container_options["environment"] = merge_environment(container_options)
if self.can_be_built():
container_options["image"] = self.full_name
else:
container_options["image"] = self._get_image_name(container_options["image"])
# Delete options which are only used when starting
for key in DOCKER_START_KEYS:
container_options.pop(key, None)
return container_options
|
https://github.com/docker/compose/issues/927
|
$ fig run -e BLA=bla bliep
Traceback (most recent call last):
File "/usr/local/bin/fig", line 9, in <module>
load_entry_point('fig==1.0.1', 'console_scripts', 'fig')()
File "/usr/local/lib/python2.7/site-packages/fig/cli/main.py", line 31, in main
command.sys_dispatch()
File "/usr/local/lib/python2.7/site-packages/fig/cli/docopt_command.py", line 21, in sys_dispatch
self.dispatch(sys.argv[1:], None)
File "/usr/local/lib/python2.7/site-packages/fig/cli/command.py", line 28, in dispatch
super(Command, self).dispatch(*args, **kwargs)
File "/usr/local/lib/python2.7/site-packages/fig/cli/docopt_command.py", line 24, in dispatch
self.perform_command(*self.parse(argv, global_options))
File "/usr/local/lib/python2.7/site-packages/fig/cli/command.py", line 56, in perform_command
handler(project, command_options)
File "/usr/local/lib/python2.7/site-packages/fig/cli/main.py", line 312, in run
service.options['environment'][k] = v
TypeError: list indices must be integers, not unicode
|
TypeError
|
def from_n3(s, default=None, backend=None, nsm=None):
r'''
Creates the Identifier corresponding to the given n3 string.
>>> from_n3('<http://ex.com/foo>') == URIRef('http://ex.com/foo')
True
>>> from_n3('"foo"@de') == Literal('foo', lang='de')
True
>>> from_n3('"""multi\nline\nstring"""@en') == Literal(
... 'multi\nline\nstring', lang='en')
True
>>> from_n3('42') == Literal(42)
True
>>> from_n3(Literal(42).n3()) == Literal(42)
True
>>> from_n3('"42"^^xsd:integer') == Literal(42)
True
>>> from rdflib import RDFS
>>> from_n3('rdfs:label') == RDFS['label']
True
>>> nsm = NamespaceManager(Graph())
>>> nsm.bind('dbpedia', 'http://dbpedia.org/resource/')
>>> berlin = URIRef('http://dbpedia.org/resource/Berlin')
>>> from_n3('dbpedia:Berlin', nsm=nsm) == berlin
True
'''
if not s:
return default
if s.startswith("<"):
return URIRef(s[1:-1])
elif s.startswith('"'):
if s.startswith('"""'):
quotes = '"""'
else:
quotes = '"'
value, rest = s.rsplit(quotes, 1)
value = value[len(quotes) :] # strip leading quotes
datatype = None
language = None
# as a given datatype overrules lang-tag check for it first
dtoffset = rest.rfind("^^")
if dtoffset >= 0:
# found a datatype
# datatype has to come after lang-tag so ignore everything before
# see: http://www.w3.org/TR/2011/WD-turtle-20110809/
# #prod-turtle2-RDFLiteral
datatype = from_n3(rest[dtoffset + 2 :], default, backend, nsm)
else:
if rest.startswith("@"):
language = rest[1:] # strip leading at sign
value = value.replace(r"\"", '"')
# Hack: this should correctly handle strings with either native unicode
# characters, or \u1234 unicode escapes.
value = value.encode("raw-unicode-escape").decode("unicode-escape")
return Literal(value, language, datatype)
elif s == "true" or s == "false":
return Literal(s == "true")
elif s.isdigit():
return Literal(int(s))
elif s.startswith("{"):
identifier = from_n3(s[1:-1])
return QuotedGraph(backend, identifier)
elif s.startswith("["):
identifier = from_n3(s[1:-1])
return Graph(backend, identifier)
elif s.startswith("_:"):
return BNode(s[2:])
elif ":" in s:
if nsm is None:
# instantiate default NamespaceManager and rely on its defaults
nsm = NamespaceManager(Graph())
prefix, last_part = s.split(":", 1)
ns = dict(nsm.namespaces())[prefix]
return Namespace(ns)[last_part]
else:
return BNode(s)
|
def from_n3(s, default=None, backend=None, nsm=None):
r'''
Creates the Identifier corresponding to the given n3 string.
>>> from_n3('<http://ex.com/foo>') == URIRef('http://ex.com/foo')
True
>>> from_n3('"foo"@de') == Literal('foo', lang='de')
True
>>> from_n3('"""multi\nline\nstring"""@en') == Literal(
... 'multi\nline\nstring', lang='en')
True
>>> from_n3('42') == Literal(42)
True
>>> from_n3(Literal(42).n3()) == Literal(42)
True
>>> from_n3('"42"^^xsd:integer') == Literal(42)
True
>>> from rdflib import RDFS
>>> from_n3('rdfs:label') == RDFS['label']
True
>>> nsm = NamespaceManager(Graph())
>>> nsm.bind('dbpedia', 'http://dbpedia.org/resource/')
>>> berlin = URIRef('http://dbpedia.org/resource/Berlin')
>>> from_n3('dbpedia:Berlin', nsm=nsm) == berlin
True
'''
if not s:
return default
if s.startswith("<"):
return URIRef(s[1:-1])
elif s.startswith('"'):
if s.startswith('"""'):
quotes = '"""'
else:
quotes = '"'
value, rest = s.rsplit(quotes, 1)
value = value[len(quotes) :] # strip leading quotes
datatype = None
language = None
# as a given datatype overrules lang-tag check for it first
dtoffset = rest.rfind("^^")
if dtoffset >= 0:
# found a datatype
# datatype has to come after lang-tag so ignore everything before
# see: http://www.w3.org/TR/2011/WD-turtle-20110809/
# #prod-turtle2-RDFLiteral
datatype = from_n3(rest[dtoffset + 2 :], default, backend, nsm)
else:
if rest.startswith("@"):
language = rest[1:] # strip leading at sign
value = value.replace(r"\"", '"').replace("\\\\", "\\")
# Hack: this should correctly handle strings with either native unicode
# characters, or \u1234 unicode escapes.
value = value.encode("raw-unicode-escape").decode("unicode-escape")
return Literal(value, language, datatype)
elif s == "true" or s == "false":
return Literal(s == "true")
elif s.isdigit():
return Literal(int(s))
elif s.startswith("{"):
identifier = from_n3(s[1:-1])
return QuotedGraph(backend, identifier)
elif s.startswith("["):
identifier = from_n3(s[1:-1])
return Graph(backend, identifier)
elif s.startswith("_:"):
return BNode(s[2:])
elif ":" in s:
if nsm is None:
# instantiate default NamespaceManager and rely on its defaults
nsm = NamespaceManager(Graph())
prefix, last_part = s.split(":", 1)
ns = dict(nsm.namespaces())[prefix]
return Namespace(ns)[last_part]
else:
return BNode(s)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def ComponentTerms(cls):
"""
Takes a Class instance and returns a generator over the classes that
are involved in its definition, ignoring unnamed classes
"""
if OWL_NS.Restriction in cls.type:
try:
cls = CastClass(cls, Individual.factoryGraph)
for s, p, innerClsId in cls.factoryGraph.triples_choices(
(cls.identifier, [OWL_NS.allValuesFrom, OWL_NS.someValuesFrom], None)
):
innerCls = Class(innerClsId, skipOWLClassMembership=True)
if isinstance(innerClsId, BNode):
for _c in ComponentTerms(innerCls):
yield _c
else:
yield innerCls
except:
pass
else:
cls = CastClass(cls, Individual.factoryGraph)
if isinstance(cls, BooleanClass):
for _cls in cls:
_cls = Class(_cls, skipOWLClassMembership=True)
if isinstance(_cls.identifier, BNode):
for _c in ComponentTerms(_cls):
yield _c
else:
yield _cls
else:
for innerCls in cls.subClassOf:
if isinstance(innerCls.identifier, BNode):
for _c in ComponentTerms(innerCls):
yield _c
else:
yield innerCls
for s, p, o in cls.factoryGraph.triples_choices(
(classOrIdentifier(cls), CLASS_RELATIONS, None)
):
if isinstance(o, BNode):
for _c in ComponentTerms(CastClass(o, Individual.factoryGraph)):
yield _c
else:
yield innerCls
|
def ComponentTerms(cls):
"""
Takes a Class instance and returns a generator over the classes that
are involved in its definition, ignoring unamed classes
"""
if OWL_NS.Restriction in cls.type:
try:
cls = CastClass(cls, Individual.factoryGraph)
for s, p, innerClsId in cls.factoryGraph.triples_choices(
(cls.identifier, [OWL_NS.allValuesFrom, OWL_NS.someValuesFrom], None)
):
innerCls = Class(innerClsId, skipOWLClassMembership=True)
if isinstance(innerClsId, BNode):
for _c in ComponentTerms(innerCls):
yield _c
else:
yield innerCls
except:
pass
else:
cls = CastClass(cls, Individual.factoryGraph)
if isinstance(cls, BooleanClass):
for _cls in cls:
_cls = Class(_cls, skipOWLClassMembership=True)
if isinstance(_cls.identifier, BNode):
for _c in ComponentTerms(_cls):
yield _c
else:
yield _cls
else:
for innerCls in cls.subClassOf:
if isinstance(innerCls.identifier, BNode):
for _c in ComponentTerms(innerCls):
yield _c
else:
yield innerCls
for s, p, o in cls.factoryGraph.triples_choices(
(classOrIdentifier(cls), CLASS_RELATIONS, None)
):
if isinstance(o, BNode):
for _c in ComponentTerms(CastClass(o, Individual.factoryGraph)):
yield _c
else:
yield innerCls
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def title(self):
# overrides unicode.title to allow DCTERMS.title for example
return URIRef(self + "title")
|
def title(self):
return URIRef(self + "title")
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def term(self, name):
uri = self.__uris.get(name)
if uri is None:
raise Exception("term '%s' not in namespace '%s'" % (name, self))
else:
return uri
|
def term(self, name):
uri = self.__uris.get(name)
if uri is None:
raise Exception("term '%s' not in namespace '%s'" % (name, self.uri))
else:
return uri
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def __repr__(self):
return """rdf.namespace.ClosedNamespace('%s')""" % self
|
def __repr__(self):
return """rdf.namespace.ClosedNamespace('%s')""" % str(self.uri)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def term(self, name):
try:
i = int(name)
return URIRef("%s_%s" % (self, i))
except ValueError:
return super(_RDFNamespace, self).term(name)
|
def term(self, name):
try:
i = int(name)
return URIRef("%s_%s" % (self.uri, i))
except ValueError:
return super(_RDFNamespace, self).term(name)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def __new__(cls):
return ClosedNamespace.__new__(
cls,
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
terms=[
# Syntax Names
"RDF",
"Description",
"ID",
"about",
"parseType",
"resource",
"li",
"nodeID",
"datatype",
# RDF Classes
"Seq",
"Bag",
"Alt",
"Statement",
"Property",
"List",
"PlainLiteral",
# RDF Properties
"subject",
"predicate",
"object",
"type",
"value",
"first",
"rest",
# and _n where n is a non-negative integer
# RDF Resources
"nil",
# Added in RDF 1.1
"XMLLiteral",
"HTML",
"langString",
],
)
|
def __new__(cls, value):
try:
rt = unicode.__new__(cls, value)
except UnicodeDecodeError:
rt = unicode.__new__(cls, value, "utf-8")
return rt
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def __init__(self, system_id=None):
xmlreader.InputSource.__init__(self, system_id=system_id)
self.content_type = None
self.auto_close = False # see Graph.parse(), true if opened by us
|
def __init__(self, system_id=None):
xmlreader.InputSource.__init__(self, system_id=system_id)
self.content_type = None
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def create_input_source(
source=None, publicID=None, location=None, file=None, data=None, format=None
):
"""
Return an appropriate InputSource instance for the given
parameters.
"""
# test that exactly one of source, location, file, and data is not None.
if (
sum(
(
source is not None,
location is not None,
file is not None,
data is not None,
)
)
!= 1
):
raise ValueError("exactly one of source, location, file or data must be given")
input_source = None
if source is not None:
if isinstance(source, InputSource):
input_source = source
else:
if isinstance(source, basestring):
location = source
elif hasattr(source, "read") and not isinstance(source, Namespace):
f = source
input_source = InputSource()
input_source.setByteStream(f)
if f is sys.stdin:
input_source.setSystemId("file:///dev/stdin")
elif hasattr(f, "name"):
input_source.setSystemId(f.name)
else:
raise Exception(
"Unexpected type '%s' for source '%s'" % (type(source), source)
)
absolute_location = None # Further to fix for issue 130
auto_close = False # make sure we close all file handles we open
if location is not None:
# Fix for Windows problem https://github.com/RDFLib/rdflib/issues/145
if os.path.exists(location):
location = pathname2url(location)
base = urljoin("file:", "%s/" % pathname2url(os.getcwd()))
absolute_location = URIRef(location, base=base).defrag()
if absolute_location.startswith("file:///"):
filename = url2pathname(absolute_location.replace("file:///", "/"))
file = open(filename, "rb")
else:
input_source = URLInputSource(absolute_location, format)
auto_close = True
# publicID = publicID or absolute_location # Further to fix
# for issue 130
if file is not None:
input_source = FileInputSource(file)
if data is not None:
if isinstance(data, unicode):
data = data.encode("utf-8")
input_source = StringInputSource(data)
auto_close = True
if input_source is None:
raise Exception("could not create InputSource")
else:
input_source.auto_close |= auto_close
if publicID is not None: # Further to fix for issue 130
input_source.setPublicId(publicID)
# Further to fix for issue 130
elif input_source.getPublicId() is None:
input_source.setPublicId(absolute_location or "")
return input_source
|
def create_input_source(
source=None, publicID=None, location=None, file=None, data=None, format=None
):
"""
Return an appropriate InputSource instance for the given
parameters.
"""
# TODO: test that exactly one of source, location, file, and data
# is not None.
input_source = None
if source is not None:
if isinstance(source, InputSource):
input_source = source
else:
if isinstance(source, basestring):
location = source
elif hasattr(source, "read") and not isinstance(source, Namespace):
f = source
input_source = InputSource()
input_source.setByteStream(f)
if f is sys.stdin:
input_source.setSystemId("file:///dev/stdin")
elif hasattr(f, "name"):
input_source.setSystemId(f.name)
else:
raise Exception(
"Unexpected type '%s' for source '%s'" % (type(source), source)
)
absolute_location = None # Further to fix for issue 130
if location is not None:
# Fix for Windows problem https://github.com/RDFLib/rdflib/issues/145
if os.path.exists(location):
location = pathname2url(location)
base = urljoin("file:", "%s/" % pathname2url(os.getcwd()))
absolute_location = URIRef(location, base=base).defrag()
if absolute_location.startswith("file:///"):
filename = url2pathname(absolute_location.replace("file:///", "/"))
file = open(filename, "rb")
else:
input_source = URLInputSource(absolute_location, format)
# publicID = publicID or absolute_location # Further to fix
# for issue 130
if file is not None:
input_source = FileInputSource(file)
if data is not None:
if isinstance(data, unicode):
data = data.encode("utf-8")
input_source = StringInputSource(data)
if input_source is None:
raise Exception("could not create InputSource")
else:
if publicID is not None: # Further to fix for issue 130
input_source.setPublicId(publicID)
# Further to fix for issue 130
elif input_source.getPublicId() is None:
input_source.setPublicId(absolute_location or "")
return input_source
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def __init__(self, name):
"""
@param name: URL to be opened
@keyword additional_headers: additional HTTP request headers to be added to the call
"""
try:
# Note the removal of the fragment ID. This is necessary, per the HTTP spec
req = Request(url=name.split("#")[0])
req.add_header("Accept", "text/html, application/xhtml+xml")
self.data = urlopen(req)
self.headers = self.data.info()
if URIOpener.CONTENT_LOCATION in self.headers:
self.location = urljoin(
self.data.geturl(), self.headers[URIOpener.CONTENT_LOCATION]
)
else:
self.location = name
except urllib_HTTPError:
e = sys.exc_info()[1]
from pyMicrodata import HTTPError
msg = BaseHTTPRequestHandler.responses[e.code]
raise HTTPError("%s" % msg[1], e.code)
except Exception:
e = sys.exc_info()[1]
from pyMicrodata import MicrodataError
raise MicrodataError("%s" % e)
|
def __init__(self, name):
"""
@param name: URL to be opened
@keyword additional_headers: additional HTTP request headers to be added to the call
"""
try:
# Note the removal of the fragment ID. This is necessary, per the HTTP spec
req = Request(url=name.split("#")[0])
req.add_header("Accept", "text/html, application/xhtml+xml")
self.data = urlopen(req)
self.headers = self.data.info()
if URIOpener.CONTENT_LOCATION in self.headers:
self.location = urlparse.urljoin(
self.data.geturl(), self.headers[URIOpener.CONTENT_LOCATION]
)
else:
self.location = name
except urllib_HTTPError:
e = sys.exc_info()[1]
from pyMicrodata import HTTPError
msg = BaseHTTPRequestHandler.responses[e.code]
raise HTTPError("%s" % msg[1], e.code)
except Exception:
e = sys.exc_info()[1]
from pyMicrodata import MicrodataError
raise MicrodataError("%s" % e)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def html5_extra_attributes(node, state):
"""
@param node: the current node that could be modified
@param state: current state
@type state: L{Execution context<pyRdfa.state.ExecutionContext>}
"""
def _get_literal(Pnode):
"""
Get (recursively) the full text from a DOM Node.
@param Pnode: DOM Node
@return: string
"""
rc = ""
for node in Pnode.childNodes:
if node.nodeType == node.TEXT_NODE:
rc = rc + node.data
elif node.nodeType == node.ELEMENT_NODE:
rc = rc + _get_literal(node)
if state.options.space_preserve:
return rc
else:
return re.sub(r"(\r| |\n|\t)+", " ", rc).strip()
# return re.sub(r'(\r| |\n|\t)+',"",rc).strip()
# end _getLiteral
def _set_time(value):
if not node.hasAttribute("datatype"):
# Check the datatype:
dt = _format_test(value)
if dt != plain:
node.setAttribute("datatype", dt)
# Finally, set the value itself
node.setAttribute("content", value)
# end _set_time
if not node.hasAttribute("content"):
# @content has top priority over the others...
if node.hasAttribute("datetime"):
_set_time(node.getAttribute("datetime"))
elif node.hasAttribute("dateTime"):
_set_time(node.getAttribute("dateTime"))
elif node.tagName == "time":
# Note that a possible @datetime value has already been taken care of
_set_time(_get_literal(node))
|
def html5_extra_attributes(node, state):
"""
@param node: the current node that could be modified
@param state: current state
@type state: L{Execution context<pyRdfa.state.ExecutionContext>}
"""
def _get_literal(Pnode):
"""
Get (recursively) the full text from a DOM Node.
@param Pnode: DOM Node
@return: string
"""
rc = ""
for node in Pnode.childNodes:
if node.nodeType == node.TEXT_NODE:
rc = rc + node.data
elif node.nodeType == node.ELEMENT_NODE:
rc = rc + self._get_literal(node)
if state.options.space_preserve:
return rc
else:
return re.sub(r"(\r| |\n|\t)+", " ", rc).strip()
# return re.sub(r'(\r| |\n|\t)+',"",rc).strip()
# end _getLiteral
def _set_time(value):
if not node.hasAttribute("datatype"):
# Check the datatype:
dt = _format_test(value)
if dt != plain:
node.setAttribute("datatype", dt)
# Finally, set the value itself
node.setAttribute("content", value)
# end _set_time
if not node.hasAttribute("content"):
# @content has top priority over the others...
if node.hasAttribute("datetime"):
_set_time(node.getAttribute("datetime"))
elif node.hasAttribute("dateTime"):
_set_time(node.getAttribute("dateTime"))
elif node.tagName == "time":
# Note that a possible @datetime value has already been taken care of
_set_time(_get_literal(node))
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def _get_literal(Pnode):
"""
Get (recursively) the full text from a DOM Node.
@param Pnode: DOM Node
@return: string
"""
rc = ""
for node in Pnode.childNodes:
if node.nodeType == node.TEXT_NODE:
rc = rc + node.data
elif node.nodeType == node.ELEMENT_NODE:
rc = rc + _get_literal(node)
if state.options.space_preserve:
return rc
else:
return re.sub(r"(\r| |\n|\t)+", " ", rc).strip()
|
def _get_literal(Pnode):
"""
Get (recursively) the full text from a DOM Node.
@param Pnode: DOM Node
@return: string
"""
rc = ""
for node in Pnode.childNodes:
if node.nodeType == node.TEXT_NODE:
rc = rc + node.data
elif node.nodeType == node.ELEMENT_NODE:
rc = rc + self._get_literal(node)
if state.options.space_preserve:
return rc
else:
return re.sub(r"(\r| |\n|\t)+", " ", rc).strip()
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def generate_1_1(self):
"""Generate the property object, 1.1 version"""
#########################################################################
# See if the target is _not_ a literal
irirefs = ("resource", "href", "src")
noiri = ("content", "datatype", "rel", "rev")
notypediri = ("content", "datatype", "rel", "rev", "about", "about_pruned")
if has_one_of_attributes(self.node, irirefs) and not has_one_of_attributes(
self.node, noiri
):
# @href/@resource/@src takes the lead here...
object = self.state.getResource(irirefs)
elif (
self.node.hasAttribute("typeof")
and not has_one_of_attributes(self.node, notypediri)
and self.typed_resource != None
):
# a @typeof creates a special branch in case the typed resource was set during parsing
object = self.typed_resource
else:
# We have to generate a literal
# Get, if exists, the value of @datatype
datatype = ""
dtset = False
if self.node.hasAttribute("datatype"):
dtset = True
dt = self.node.getAttribute("datatype")
if dt != "":
datatype = self.state.getURI("datatype")
# Supress lange is set in case some elements explicitly want to supress the effect of language
# There were discussions, for example, that the <time> element should do so. Although,
# after all, this was reversed, the functionality is kept in the code in case another
# element might need it...
if self.state.lang != None and self.state.supress_lang == False:
lang = self.state.lang
else:
lang = ""
# The simple case: separate @content attribute
if self.node.hasAttribute("content"):
val = self.node.getAttribute("content")
# Handling the automatic uri conversion case
if dtset == False:
object = Literal(val, lang=lang)
else:
object = self._create_Literal(val, datatype=datatype, lang=lang)
# The value of datatype has been set, and the keyword parameters take care of the rest
else:
# see if there *is* a datatype (even if it is empty!)
if dtset:
if datatype == XMLLiteral:
litval = self._get_XML_literal(self.node)
object = Literal(litval, datatype=XMLLiteral)
elif datatype == HTMLLiteral:
# I am not sure why this hack is necessary, but otherwise an encoding error occurs
# In Python3 all this should become moot, due to the unicode everywhere approach...
if sys.version_info[0] >= 3:
object = Literal(
self._get_HTML_literal(self.node), datatype=HTMLLiteral
)
else:
litval = self._get_HTML_literal(self.node)
o = Literal(litval, datatype=XMLLiteral)
object = Literal(o, datatype=HTMLLiteral)
else:
object = self._create_Literal(
self._get_literal(self.node), datatype=datatype, lang=lang
)
else:
object = self._create_Literal(self._get_literal(self.node), lang=lang)
if object != None:
for prop in self.state.getURI("property"):
if not isinstance(prop, BNode):
if self.node.hasAttribute("inlist"):
self.state.add_to_list_mapping(prop, object)
else:
self.graph.add((self.subject, prop, object))
else:
self.state.options.add_warning(
err_no_blank_node % "property",
warning_type=IncorrectBlankNodeUsage,
node=self.node.nodeName,
)
|
def generate_1_1(self):
"""Generate the property object, 1.1 version"""
#########################################################################
# See if the target is _not_ a literal
irirefs = ("resource", "href", "src")
noiri = ("content", "datatype", "rel", "rev")
notypediri = ("content", "datatype", "rel", "rev", "about", "about_pruned")
if has_one_of_attributes(self.node, irirefs) and not has_one_of_attributes(
self.node, noiri
):
# @href/@resource/@src takes the lead here...
object = self.state.getResource(irirefs)
elif (
self.node.hasAttribute("typeof")
and not has_one_of_attributes(self.node, notypediri)
and self.typed_resource != None
):
# a @typeof creates a special branch in case the typed resource was set during parsing
object = self.typed_resource
else:
# We have to generate a literal
# Get, if exists, the value of @datatype
datatype = ""
dtset = False
if self.node.hasAttribute("datatype"):
dtset = True
dt = self.node.getAttribute("datatype")
if dt != "":
datatype = self.state.getURI("datatype")
# Supress lange is set in case some elements explicitly want to supress the effect of language
# There were discussions, for example, that the <time> element should do so. Although,
# after all, this was reversed, the functionality is kept in the code in case another
# element might need it...
if self.state.lang != None and self.state.supress_lang == False:
lang = self.state.lang
else:
lang = ""
# The simple case: separate @content attribute
if self.node.hasAttribute("content"):
val = self.node.getAttribute("content")
# Handling the automatic uri conversion case
if dtset == False:
object = Literal(val, lang=lang)
else:
object = self._create_Literal(val, datatype=datatype, lang=lang)
# The value of datatype has been set, and the keyword paramaters take care of the rest
else:
# see if there *is* a datatype (even if it is empty!)
if dtset:
if datatype == XMLLiteral:
litval = self._get_XML_literal(self.node)
object = Literal(litval, datatype=XMLLiteral)
elif datatype == HTMLLiteral:
# I am not sure why this hack is necessary, but otherwise an encoding error occurs
# In Python3 all this should become moot, due to the unicode everywhere approach...
if sys.version_info[0] >= 3:
object = Literal(
self._get_HTML_literal(self.node), datatype=HTMLLiteral
)
else:
litval = self._get_HTML_literal(self.node)
o = Literal(litval, datatype=XMLLiteral)
object = Literal(o, datatype=HTMLLiteral)
else:
object = self._create_Literal(
self._get_literal(self.node), datatype=datatype, lang=lang
)
else:
object = self._create_Literal(self._get_literal(self.node), lang=lang)
if object != None:
for prop in self.state.getURI("property"):
if not isinstance(prop, BNode):
if self.node.hasAttribute("inlist"):
self.state.add_to_list_mapping(prop, object)
else:
self.graph.add((self.subject, prop, object))
else:
self.state.options.add_warning(
err_no_blank_node % "property",
warning_type=IncorrectBlankNodeUsage,
node=self.node.nodeName,
)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def generate_1_0(self):
"""Generate the property object, 1.0 version"""
#########################################################################
# We have to generate a literal indeed.
# Get, if exists, the value of @datatype
datatype = ""
dtset = False
if self.node.hasAttribute("datatype"):
dtset = True
dt = self.node.getAttribute("datatype")
if dt != "":
datatype = self.state.getURI("datatype")
if self.state.lang != None:
lang = self.state.lang
else:
lang = ""
# The simple case: separate @content attribute
if self.node.hasAttribute("content"):
val = self.node.getAttribute("content")
# Handling the automatic uri conversion case
if dtset == False:
object = Literal(val, lang=lang)
else:
object = self._create_Literal(val, datatype=datatype, lang=lang)
# The value of datatype has been set, and the keyword parameters take care of the rest
else:
# see if there *is* a datatype (even if it is empty!)
if dtset:
# yep. The Literal content is the pure text part of the current element:
# We have to check whether the specified datatype is, in fact, an
# explicit XML Literal
if datatype == XMLLiteral:
litval = self._get_XML_literal(self.node)
object = Literal(litval, datatype=XMLLiteral)
elif datatype == HTMLLiteral:
# I am not sure why this hack is necessary, but otherwise an encoding error occurs
# In Python3 all this should become moot, due to the unicode everywhere approach...
if sys.version_info[0] >= 3:
object = Literal(
self._get_HTML_literal(self.node), datatype=HTMLLiteral
)
else:
litval = self._get_HTML_literal(self.node)
o = Literal(litval, datatype=XMLLiteral)
object = Literal(o, datatype=HTMLLiteral)
else:
object = self._create_Literal(
self._get_literal(self.node), datatype=datatype, lang=lang
)
else:
# no controlling @datatype. We have to see if there is markup in the contained
# element
if True in [
n.nodeType == self.node.ELEMENT_NODE for n in self.node.childNodes
]:
# yep, and XML Literal should be generated
object = self._create_Literal(
self._get_XML_literal(self.node), datatype=XMLLiteral
)
else:
# At this point, there might be entities in the string that are returned as real characters by the dom
# implementation. That should be turned back
object = self._create_Literal(self._get_literal(self.node), lang=lang)
for prop in self.state.getURI("property"):
if not isinstance(prop, BNode):
self.graph.add((self.subject, prop, object))
else:
self.state.options.add_warning(
err_no_blank_node % "property",
warning_type=IncorrectBlankNodeUsage,
node=self.node.nodeName,
)
|
def generate_1_0(self):
"""Generate the property object, 1.0 version"""
#########################################################################
# We have to generate a literal indeed.
# Get, if exists, the value of @datatype
datatype = ""
dtset = False
if self.node.hasAttribute("datatype"):
dtset = True
dt = self.node.getAttribute("datatype")
if dt != "":
datatype = self.state.getURI("datatype")
if self.state.lang != None:
lang = self.state.lang
else:
lang = ""
# The simple case: separate @content attribute
if self.node.hasAttribute("content"):
val = self.node.getAttribute("content")
# Handling the automatic uri conversion case
if dtset == False:
object = Literal(val, lang=lang)
else:
object = self._create_Literal(val, datatype=datatype, lang=lang)
# The value of datatype has been set, and the keyword paramaters take care of the rest
else:
# see if there *is* a datatype (even if it is empty!)
if dtset:
# yep. The Literal content is the pure text part of the current element:
# We have to check whether the specified datatype is, in fact, an
# explicit XML Literal
if datatype == XMLLiteral:
litval = self._get_XML_literal(self.node)
object = Literal(litval, datatype=XMLLiteral)
elif datatype == HTMLLiteral:
# I am not sure why this hack is necessary, but otherwise an encoding error occurs
# In Python3 all this should become moot, due to the unicode everywhere approach...
if sys.version_info[0] >= 3:
object = Literal(
self._get_HTML_literal(self.node), datatype=HTMLLiteral
)
else:
litval = self._get_HTML_literal(self.node)
o = Literal(litval, datatype=XMLLiteral)
object = Literal(o, datatype=HTMLLiteral)
else:
object = self._create_Literal(
self._get_literal(self.node), datatype=datatype, lang=lang
)
else:
# no controlling @datatype. We have to see if there is markup in the contained
# element
if True in [
n.nodeType == self.node.ELEMENT_NODE for n in self.node.childNodes
]:
# yep, and XML Literal should be generated
object = self._create_Literal(
self._get_XML_literal(self.node), datatype=XMLLiteral
)
else:
# At this point, there might be entities in the string that are returned as real characters by the dom
# implementation. That should be turned back
object = self._create_Literal(self._get_literal(self.node), lang=lang)
for prop in self.state.getURI("property"):
if not isinstance(prop, BNode):
self.graph.add((self.subject, prop, object))
else:
self.state.options.add_warning(
err_no_blank_node % "property",
warning_type=IncorrectBlankNodeUsage,
node=self.node.nodeName,
)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def evalPart(ctx, part):
# try custom evaluation functions
for name, c in CUSTOM_EVALS.items():
try:
return c(ctx, part)
except NotImplementedError:
pass # the given custome-function did not handle this part
if part.name == "BGP":
# Reorder triples patterns by number of bound nodes in the current ctx
# Do patterns with more bound nodes first
triples = sorted(
part.triples, key=lambda t: len([n for n in t if ctx[n] is None])
)
return evalBGP(ctx, triples)
elif part.name == "Filter":
return evalFilter(ctx, part)
elif part.name == "Join":
return evalJoin(ctx, part)
elif part.name == "LeftJoin":
return evalLeftJoin(ctx, part)
elif part.name == "Graph":
return evalGraph(ctx, part)
elif part.name == "Union":
return evalUnion(ctx, part)
elif part.name == "ToMultiSet":
return evalMultiset(ctx, part)
elif part.name == "Extend":
return evalExtend(ctx, part)
elif part.name == "Minus":
return evalMinus(ctx, part)
elif part.name == "Project":
return evalProject(ctx, part)
elif part.name == "Slice":
return evalSlice(ctx, part)
elif part.name == "Distinct":
return evalDistinct(ctx, part)
elif part.name == "Reduced":
return evalReduced(ctx, part)
elif part.name == "OrderBy":
return evalOrderBy(ctx, part)
elif part.name == "Group":
return evalGroup(ctx, part)
elif part.name == "AggregateJoin":
return evalAggregateJoin(ctx, part)
elif part.name == "SelectQuery":
return evalSelectQuery(ctx, part)
elif part.name == "AskQuery":
return evalAskQuery(ctx, part)
elif part.name == "ConstructQuery":
return evalConstructQuery(ctx, part)
elif part.name == "ServiceGraphPattern":
raise Exception("ServiceGraphPattern not implemented")
elif part.name == "DescribeQuery":
raise Exception("DESCRIBE not implemented")
else:
# import pdb ; pdb.set_trace()
raise Exception("I dont know: %s" % part.name)
|
def evalPart(ctx, part):
# try custom evaluation functions
for name, c in CUSTOM_EVALS.items():
try:
return c(ctx, part)
except NotImplementedError:
pass # the given custome-function did not handle this part
if part.name == "BGP":
return evalBGP(ctx, part.triples) # NOTE pass part.triples, not part!
elif part.name == "Filter":
return evalFilter(ctx, part)
elif part.name == "Join":
return evalJoin(ctx, part)
elif part.name == "LeftJoin":
return evalLeftJoin(ctx, part)
elif part.name == "Graph":
return evalGraph(ctx, part)
elif part.name == "Union":
return evalUnion(ctx, part)
elif part.name == "ToMultiSet":
return evalMultiset(ctx, part)
elif part.name == "Extend":
return evalExtend(ctx, part)
elif part.name == "Minus":
return evalMinus(ctx, part)
elif part.name == "Project":
return evalProject(ctx, part)
elif part.name == "Slice":
return evalSlice(ctx, part)
elif part.name == "Distinct":
return evalDistinct(ctx, part)
elif part.name == "Reduced":
return evalReduced(ctx, part)
elif part.name == "OrderBy":
return evalOrderBy(ctx, part)
elif part.name == "Group":
return evalGroup(ctx, part)
elif part.name == "AggregateJoin":
return evalAggregateJoin(ctx, part)
elif part.name == "SelectQuery":
return evalSelectQuery(ctx, part)
elif part.name == "AskQuery":
return evalAskQuery(ctx, part)
elif part.name == "ConstructQuery":
return evalConstructQuery(ctx, part)
elif part.name == "ServiceGraphPattern":
raise Exception("ServiceGraphPattern not implemented")
elif part.name == "DescribeQuery":
raise Exception("DESCRIBE not implemented")
else:
# import pdb ; pdb.set_trace()
raise Exception("I dont know: %s" % part.name)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def evalQuery(graph, query, initBindings, base=None):
ctx = QueryContext(graph)
ctx.prologue = query.prologue
main = query.algebra
if initBindings:
# add initBindings as a values clause
values = {} # no dict comprehension in 2.6 :(
for k, v in initBindings.iteritems():
if not isinstance(k, Variable):
k = Variable(k)
values[k] = v
main = main.clone() # clone to not change prepared q
main["p"] = main.p.clone()
# Find the right place to insert MultiSet join
repl = main.p
if repl.name == "Slice":
repl["p"] = repl.p.clone()
repl = repl.p
if repl.name == "Distinct":
repl["p"] = repl.p.clone()
repl = repl.p
if repl.p.name == "OrderBy":
repl["p"] = repl.p.clone()
repl = repl.p
if repl.p.name == "Extend":
repl["p"] = repl.p.clone()
repl = repl.p
repl["p"] = Join(repl.p, ToMultiSet(Values([values])))
# TODO: Vars?
if main.datasetClause:
if ctx.dataset is None:
raise Exception(
"Non-conjunctive-graph doesn't know about "
+ "graphs! Try a query without FROM (NAMED)."
)
ctx = ctx.clone() # or push/pop?
firstDefault = False
for d in main.datasetClause:
if d.default:
if firstDefault:
# replace current default graph
dg = ctx.dataset.get_context(BNode())
ctx = ctx.pushGraph(dg)
firstDefault = True
ctx.load(d.default, default=True)
elif d.named:
g = d.named
ctx.load(g, default=False)
return evalPart(ctx, main)
|
def evalQuery(graph, query, initBindings, base=None):
ctx = QueryContext(graph)
ctx.prologue = query.prologue
if initBindings:
for k, v in initBindings.iteritems():
if not isinstance(k, Variable):
k = Variable(k)
ctx[k] = v
# ctx.push() # nescessary?
main = query.algebra
# import pdb; pdb.set_trace()
if main.datasetClause:
if ctx.dataset is None:
raise Exception(
"Non-conjunctive-graph doesn't know about "
+ "graphs! Try a query without FROM (NAMED)."
)
ctx = ctx.clone() # or push/pop?
firstDefault = False
for d in main.datasetClause:
if d.default:
if firstDefault:
# replace current default graph
dg = ctx.dataset.get_context(BNode())
ctx = ctx.pushGraph(dg)
firstDefault = True
ctx.load(d.default, default=True)
elif d.named:
g = d.named
ctx.load(g, default=False)
return evalPart(ctx, main)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def absolutize(self, iri):
"""
Apply BASE / PREFIXes to URIs
(and to datatypes in Literals)
TODO: Move resolving URIs to pre-processing
"""
if isinstance(iri, CompValue):
if iri.name == "pname":
return self.resolvePName(iri.prefix, iri.localname)
if iri.name == "literal":
return Literal(
iri.string, lang=iri.lang, datatype=self.absolutize(iri.datatype)
)
elif isinstance(iri, URIRef) and not ":" in iri:
return URIRef(iri, base=self.base)
return iri
|
def absolutize(self, iri):
"""
Apply BASE / PREFIXes to URIs
(and to datatypes in Literals)
TODO: Move resolving URIs to pre-processing
"""
if isinstance(iri, CompValue):
if iri.name == "pname":
return self.resolvePName(iri.prefix, iri.localname)
if iri.name == "literal":
return Literal(
iri.string, lang=iri.lang, datatype=self.absolutize(iri.datatype)
)
elif isinstance(iri, URIRef) and not ":" in iri: # TODO: Check for relative URI?
return URIRef(self.base + iri)
return iri
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def __getitem__(self, item):
if isinstance(item, slice):
if item.step:
raise TypeError(
"Resources fix the subject for slicing, and can only be sliced by predicate/object. "
)
p, o = item.start, item.stop
if isinstance(p, Resource):
p = p._identifier
if isinstance(o, Resource):
o = o._identifier
if p is None and o is None:
return self.predicate_objects()
elif p is None:
return self.predicates(o)
elif o is None:
return self.objects(p)
else:
return (self.identifier, p, o) in self._graph
elif isinstance(item, (Node, Path)):
return self.objects(item)
else:
raise TypeError(
"You can only index a resource by a single rdflib term, a slice of rdflib terms, not %s (%s)"
% (item, type(item))
)
|
def __getitem__(self, item):
if isinstance(item, slice):
if item.step:
raise TypeError(
"Resources fix the subject for slicing, and can only be sliced by predicate/object. "
)
p, o = item.start, item.stop
if p is None and o is None:
return self.predicate_objects()
elif p is None:
return self.predicates(o)
elif o is None:
return self.objects(p)
else:
return (self.identifier, p, o) in self._graph
elif isinstance(item, (Node, Path)):
return self.objects(item)
else:
raise TypeError(
"You can only index a resource by a single rdflib term, a slice of rdflib terms, not %s (%s)"
% (item, type(item))
)
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def setup_python3():
# Taken from "distribute" setup.py
from distutils.filelist import FileList
from distutils import dir_util, file_util, util, log
from os.path import join, exists
tmp_src = join("build", "src")
# Not covered by "setup.py clean --all", so explicit deletion required.
if exists(tmp_src):
dir_util.remove_tree(tmp_src)
# log.set_verbosity(1)
fl = FileList()
for line in open("MANIFEST.in"):
if not line.strip():
continue
fl.process_template_line(line)
dir_util.create_tree(tmp_src, fl.files)
outfiles_2to3 = []
for f in fl.files:
outf, copied = file_util.copy_file(f, join(tmp_src, f), update=1)
if copied and outf.endswith(".py"):
outfiles_2to3.append(outf)
util.run_2to3(outfiles_2to3)
# arrange setup to use the copy
sys.path.insert(0, tmp_src)
return tmp_src
|
def setup_python3():
# Taken from "distribute" setup.py
from distutils.filelist import FileList
from distutils import dir_util, file_util, util, log
from os.path import join, exists
tmp_src = join("build", "src")
# Not covered by "setup.py clean --all", so explicit deletion required.
if exists(tmp_src):
dir_util.remove_tree(tmp_src)
log.set_verbosity(1)
fl = FileList()
for line in open("MANIFEST.in"):
if not line.strip():
continue
fl.process_template_line(line)
dir_util.create_tree(tmp_src, fl.files)
outfiles_2to3 = []
for f in fl.files:
outf, copied = file_util.copy_file(f, join(tmp_src, f), update=1)
if copied and outf.endswith(".py"):
outfiles_2to3.append(outf)
util.run_2to3(outfiles_2to3)
# arrange setup to use the copy
sys.path.insert(0, tmp_src)
return tmp_src
|
https://github.com/RDFLib/rdflib/issues/546
|
from rdflib.util import from_n3
sample = "\"Sample string with trailing backslash\\\"^^xsd:string"
from_n3(sample)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.4/site-packages/rdflib/util.py", line 183, in from_n3
value = value.encode("raw-unicode-escape").decode("unicode-escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode byte 0x5c in position 37: \ at end of string
|
UnicodeDecodeError
|
def create_input_source(
source=None, publicID=None, location=None, file=None, data=None, format=None
):
"""
Return an appropriate InputSource instance for the given
parameters.
"""
# TODO: test that exactly one of source, location, file, and data
# is not None.
input_source = None
if source is not None:
if isinstance(source, InputSource):
input_source = source
else:
if isinstance(source, basestring):
location = source
elif hasattr(source, "read") and not isinstance(source, Namespace):
f = source
input_source = InputSource()
input_source.setByteStream(f)
if f is sys.stdin:
input_source.setSystemId("file:///dev/stdin")
elif hasattr(f, "name"):
input_source.setSystemId(f.name)
else:
raise Exception(
"Unexpected type '%s' for source '%s'" % (type(source), source)
)
absolute_location = None # Further to fix for issue 130
if location is not None:
# Fix for Windows problem https://github.com/RDFLib/rdflib/issues/145
if os.path.exists(location):
location = pathname2url(location)
base = urljoin("file:", "%s/" % pathname2url(os.getcwd()))
absolute_location = URIRef(location, base=base).defrag()
if absolute_location.startswith("file:///"):
filename = url2pathname(absolute_location.replace("file:///", "/"))
file = open(filename, "rb")
else:
input_source = URLInputSource(absolute_location, format)
# publicID = publicID or absolute_location # Further to fix
# for issue 130
if file is not None:
input_source = FileInputSource(file)
if data is not None:
if isinstance(data, unicode):
data = data.encode("utf-8")
input_source = StringInputSource(data)
if input_source is None:
raise Exception("could not create InputSource")
else:
if publicID is not None: # Further to fix for issue 130
input_source.setPublicId(publicID)
# Further to fix for issue 130
elif input_source.getPublicId() is None:
input_source.setPublicId(absolute_location or "")
return input_source
|
def create_input_source(
source=None, publicID=None, location=None, file=None, data=None, format=None
):
"""
Return an appropriate InputSource instance for the given
parameters.
"""
# TODO: test that exactly one of source, location, file, and data
# is not None.
input_source = None
if source is not None:
if isinstance(source, InputSource):
input_source = source
else:
if isinstance(source, basestring):
location = source
elif hasattr(source, "read") and not isinstance(source, Namespace):
f = source
input_source = InputSource()
input_source.setByteStream(f)
if hasattr(f, "name"):
input_source.setSystemId(f.name)
else:
raise Exception(
"Unexpected type '%s' for source '%s'" % (type(source), source)
)
absolute_location = None # Further to fix for issue 130
if location is not None:
# Fix for Windows problem https://github.com/RDFLib/rdflib/issues/145
if os.path.exists(location):
location = pathname2url(location)
base = urljoin("file:", "%s/" % pathname2url(os.getcwd()))
absolute_location = URIRef(location, base=base).defrag()
if absolute_location.startswith("file:///"):
filename = url2pathname(absolute_location.replace("file:///", "/"))
file = open(filename, "rb")
else:
input_source = URLInputSource(absolute_location, format)
# publicID = publicID or absolute_location # Further to fix
# for issue 130
if file is not None:
input_source = FileInputSource(file)
if data is not None:
if isinstance(data, unicode):
data = data.encode("utf-8")
input_source = StringInputSource(data)
if input_source is None:
raise Exception("could not create InputSource")
else:
if publicID is not None: # Further to fix for issue 130
input_source.setPublicId(publicID)
# Further to fix for issue 130
elif input_source.getPublicId() is None:
input_source.setPublicId(absolute_location or "")
return input_source
|
https://github.com/RDFLib/rdflib/issues/285
|
Traceback (most recent call last):
File "<string>", line 4, in <module>
...
File ".../rdflib/term.py", line 208, in __new__
raise Exception('%s does not look like a valid URI, perhaps you want to urlencode it?'%value)
Exception: file:///private/tmp/<stdin> does not look like a valid URI, perhaps you want to urlencode it?
|
Exception
|
def compute_qname(self, uri, generate=True):
if not _is_valid_uri(uri):
raise Exception(
'"%s" does not look like a valid URI, I cannot serialize this. Perhaps you wanted to urlencode it?'
% uri
)
if not uri in self.__cache:
namespace, name = split_uri(uri)
namespace = URIRef(namespace)
prefix = self.store.prefix(namespace)
if prefix is None:
if not generate:
raise Exception("No known prefix for %s and generate=False")
num = 1
while 1:
prefix = "ns%s" % num
if not self.store.namespace(prefix):
break
num += 1
self.bind(prefix, namespace)
self.__cache[uri] = (prefix, namespace, name)
return self.__cache[uri]
|
def compute_qname(self, uri, generate=True):
if not uri in self.__cache:
namespace, name = split_uri(uri)
namespace = URIRef(namespace)
prefix = self.store.prefix(namespace)
if prefix is None:
if not generate:
raise Exception("No known prefix for %s and generate=False")
num = 1
while 1:
prefix = "ns%s" % num
if not self.store.namespace(prefix):
break
num += 1
self.bind(prefix, namespace)
self.__cache[uri] = (prefix, namespace, name)
return self.__cache[uri]
|
https://github.com/RDFLib/rdflib/issues/285
|
Traceback (most recent call last):
File "<string>", line 4, in <module>
...
File ".../rdflib/term.py", line 208, in __new__
raise Exception('%s does not look like a valid URI, perhaps you want to urlencode it?'%value)
Exception: file:///private/tmp/<stdin> does not look like a valid URI, perhaps you want to urlencode it?
|
Exception
|
async def checkData(tweet, location, config, conn):
usernames = []
copyright = tweet.find("div", "StreamItemContent--withheld")
if copyright is None and is_tweet(tweet):
tweet = Tweet(tweet, location, config)
if not tweet.datestamp:
print("[x] Hidden tweet found, account suspended due to violation of TOS")
return
if datecheck(tweet.datestamp, config):
output = format.Tweet(config, tweet)
if config.Database:
db.tweets(conn, tweet, config)
if config.Pandas:
panda.update(tweet, config)
if config.Store_object:
tweets_object.append(tweet)
if config.Elasticsearch:
elasticsearch.Tweet(tweet, config)
_output(tweet, output, config)
|
async def checkData(tweet, location, config, conn):
usernames = []
user_ids = set()
global _duplicate_dict
copyright = tweet.find("div", "StreamItemContent--withheld")
if copyright is None and is_tweet(tweet):
tweet = Tweet(tweet, location, config)
if datecheck(tweet.datestamp, config):
output = format.Tweet(config, tweet)
if config.Database:
db.tweets(conn, tweet, config)
if config.Pandas:
panda.update(tweet, config)
if config.Store_object:
tweets_object.append(tweet)
if config.Elasticsearch:
elasticsearch.Tweet(tweet, config)
_output(tweet, output, config)
|
https://github.com/twintproject/twint/issues/321
|
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.6/dist-packages/twint-1.2.1-py3.6.egg/twint/run.py", line 215, in Search
File "/usr/local/lib/python3.6/dist-packages/twint-1.2.1-py3.6.egg/twint/run.py", line 167, in run
File "/usr/lib/python3.6/asyncio/base_events.py", line 473, in run_until_complete
return future.result()
File "/usr/local/lib/python3.6/dist-packages/twint-1.2.1-py3.6.egg/twint/run.py", line 154, in main
File "/usr/local/lib/python3.6/dist-packages/twint-1.2.1-py3.6.egg/twint/run.py", line 117, in tweets
File "/usr/local/lib/python3.6/dist-packages/twint-1.2.1-py3.6.egg/twint/output.py", line 118, in Tweets
File "/usr/local/lib/python3.6/dist-packages/twint-1.2.1-py3.6.egg/twint/output.py", line 96, in checkData
File "/usr/local/lib/python3.6/dist-packages/twint-1.2.1-py3.6.egg/twint/storage/db.py", line 241, in tweets
TypeError: can only join an iterable
|
TypeError
|
def _output(obj, output, config, **extra):
# logging.info("[<] " + str(datetime.now()) + ':: output+_output')
if config.Lowercase:
if isinstance(obj, str):
obj = obj.lower()
elif str(type(obj)) == "<class 'twint.user.user'>":
pass
else:
obj.username = obj.username.lower()
for i in range(len(obj.mentions)):
obj.mentions[i] = obj.mentions[i]["screen_name"].lower()
for i in range(len(obj.hashtags)):
obj.hashtags[i] = obj.hashtags[i].lower()
if config.Output != None:
if config.Store_csv:
try:
write.Csv(obj, config)
except Exception as e:
print(str(e) + " [x] output._output")
elif config.Store_json:
write.Json(obj, config)
else:
write.Text(output, config.Output)
if config.Pandas and obj.type == "user":
panda.update(obj, config)
if extra.get("follow_list"):
follow_object.username = config.Username
follow_object.action = (
config.Following * "following" + config.Followers * "followers"
)
follow_object.users = _follow_list
panda.update(follow_object, config.Essid)
if config.Elasticsearch:
print("", end=".", flush=True)
else:
if config.Store_object:
tweets_object.append(obj)
else:
if not config.Hide_output:
try:
print(output)
except UnicodeEncodeError:
print("unicode error [x] output._output")
|
def _output(obj, output, config, **extra):
# logging.info("[<] " + str(datetime.now()) + ':: output+_output')
if config.Lowercase:
if isinstance(obj, str):
obj = obj.lower()
elif str(type(obj)) == "<class 'twint.user.user'>":
pass
else:
obj.username = obj.username.lower()
for i in range(len(obj.mentions)):
obj.mentions[i] = obj.mentions[i]["screen_name"].lower()
for i in range(len(obj.hashtags)):
obj.hashtags[i] = obj.hashtags[i].lower()
if config.Output != None:
if config.Store_csv:
try:
write.Csv(obj, config)
except Exception as e:
print(str(e) + " [x] output._output")
elif config.Store_json:
write.Json(obj, config)
else:
write.Text(output, config.Output)
if config.Pandas and config.User_full:
panda.update(obj, config)
if extra.get("follow_list"):
follow_object.username = config.Username
follow_object.action = (
config.Following * "following" + config.Followers * "followers"
)
follow_object.users = _follow_list
panda.update(follow_object, config.Essid)
if config.Elasticsearch:
print("", end=".", flush=True)
else:
if config.Store_object:
tweets_object.append(obj)
else:
if not config.Hide_output:
try:
print(output)
except UnicodeEncodeError:
print("unicode error [x] output._output")
|
https://github.com/twintproject/twint/issues/283
|
Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 12:04:33)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
import twint
c = twint.Config()
query= 'bar'
c.Search = query
c.Pandas = True
twint.run.Search(c)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File ".../lib/python3.6/site-packages/twint/run.py", line 201, in Search
run(config)
File ".../lib/python3.6/site-packages/twint/run.py", line 153, in run
get_event_loop().run_until_complete(Twint(config).main())
File ".../lib/python3.6/asyncio/base_events.py", line 467, in run_until_complete
return future.result()
File ".../lib/python3.6/site-packages/twint/run.py", line 140, in main
await self.tweets()
File ".../lib/python3.6/site-packages/twint/run.py", line 103, in tweets
await output.Tweets(tweet, "", self.config, self.conn)
File ".../lib/python3.6/site-packages/twint/output.py", line 161, in Tweets
await checkData(tweets, location, config, conn)
File ".../lib/python3.6/site-packages/twint/output.py", line 142, in checkData
panda.update(tweet, config)
File ".../lib/python3.6/site-packages/twint/storage/panda.py", line 61, in update
"user_rt": object.user_rt,
AttributeError: 'tweet' object has no attribute 'user_rt'
|
AttributeError
|
def update(object, config):
global _type
try:
_type = (object.type == "tweet") * "tweet" + (object.type == "user") * "user"
except AttributeError:
_type = config.Following * "following" + config.Followers * "followers"
if _type == "tweet":
Tweet = object
day = weekdays[strftime("%A", localtime(Tweet.datetime))]
dt = f"{object.datestamp} {object.timestamp}"
_data = {
"id": str(Tweet.id),
"conversation_id": Tweet.conversation_id,
"created_at": Tweet.datetime,
"date": dt,
"timezone": Tweet.timezone,
"place": Tweet.place,
"location": Tweet.location,
"tweet": Tweet.tweet,
"hashtags": Tweet.hashtags,
"user_id": Tweet.user_id,
"user_id_str": Tweet.user_id_str,
"username": Tweet.username,
"name": Tweet.name,
"profile_image_url": Tweet.profile_image_url,
"day": day,
"hour": hour(Tweet.datetime),
"link": Tweet.link,
"gif_url": Tweet.gif_url,
"gif_thumb": Tweet.gif_thumb,
"video_url": Tweet.video_url,
"video_thumb": Tweet.video_thumb,
"is_reply_to": Tweet.is_reply_to,
"has_parent_tweet": Tweet.has_parent_tweet,
"retweet": Tweet.retweet,
"nlikes": int(Tweet.likes_count),
"nreplies": int(Tweet.replies_count),
"nretweets": int(Tweet.retweets_count),
"is_quote_status": Tweet.is_quote_status,
"quote_id": Tweet.quote_id,
"quote_id_str": Tweet.quote_id_str,
"quote_url": Tweet.quote_url,
"search": str(config.Search),
"near": config.Near,
}
_object_blocks[_type].append(_data)
elif _type == "user":
user = object
_data = {
"id": user.id,
"name": user.name,
"username": user.username,
"bio": user.bio,
"location": user.location,
"url": user.url,
"join_datetime": user.join_date + " " + user.join_time,
"join_date": user.join_date,
"join_time": user.join_time,
"tweets": user.tweets,
"following": user.following,
"followers": user.followers,
"likes": user.likes,
"media": user.media_count,
"private": user.is_private,
"verified": user.is_verified,
"avatar": user.avatar,
"background_image": user.background_image,
}
_object_blocks[_type].append(_data)
elif _type == "followers" or _type == "following":
_data = {
config.Following * "following" + config.Followers * "followers": {
config.Username: object[_type]
}
}
_object_blocks[_type] = _data
else:
print("Wrong type of object passed!")
|
def update(object, config):
global _type
try:
_type = (object.type == "tweet") * "tweet" + (object.type == "user") * "user"
except AttributeError:
_type = config.Following * "following" + config.Followers * "followers"
if _type == "tweet":
dt = f"{object.datestamp} {object.timestamp}"
_data = {
"id": object.id,
"date": dt,
"timezone": object.timezone,
"location": object.location,
"tweet": object.tweet,
"hashtags": object.hashtags,
"user_id": object.user_id,
"username": object.username,
"link": object.link,
"retweet": object.retweet,
"user_rt": object.user_rt,
"essid": config.Essid,
"mentions": object.mentions,
}
_object_blocks[_type].append(_data)
elif _type == "user":
_data = {
"id": object.id,
"name": object.name,
"username": object.username,
"bio": object.bio,
"location": object.location,
"url": object.url,
"join_datetime": object.join_date + " " + object.join_time,
"join_date": object.join_date,
"join_time": object.join_time,
"tweets": object.tweets,
"following": object.following,
"followers": object.followers,
"likes": object.likes,
"media": object.media_count,
"private": object.is_private,
"verified": object.is_verified,
"avatar": object.avatar,
"session": str(config.Essid),
}
_object_blocks[_type].append(_data)
elif _type == "followers" or _type == "following":
_data = {
config.Following * "following" + config.Followers * "followers": {
config.Username: object[_type]
}
}
_object_blocks[_type] = _data
else:
print("Wrong type of object passed!")
|
https://github.com/twintproject/twint/issues/283
|
Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 12:04:33)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
import twint
c = twint.Config()
query= 'bar'
c.Search = query
c.Pandas = True
twint.run.Search(c)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File ".../lib/python3.6/site-packages/twint/run.py", line 201, in Search
run(config)
File ".../lib/python3.6/site-packages/twint/run.py", line 153, in run
get_event_loop().run_until_complete(Twint(config).main())
File ".../lib/python3.6/asyncio/base_events.py", line 467, in run_until_complete
return future.result()
File ".../lib/python3.6/site-packages/twint/run.py", line 140, in main
await self.tweets()
File ".../lib/python3.6/site-packages/twint/run.py", line 103, in tweets
await output.Tweets(tweet, "", self.config, self.conn)
File ".../lib/python3.6/site-packages/twint/output.py", line 161, in Tweets
await checkData(tweets, location, config, conn)
File ".../lib/python3.6/site-packages/twint/output.py", line 142, in checkData
panda.update(tweet, config)
File ".../lib/python3.6/site-packages/twint/storage/panda.py", line 61, in update
"user_rt": object.user_rt,
AttributeError: 'tweet' object has no attribute 'user_rt'
|
AttributeError
|
def update(Tweet, session):
day = weekday(strftime("%A", localtime(Tweet.datetime)))
dt = "{} {}".format(Tweet.datestamp, Tweet.timestamp)
_data = {
"id": Tweet.id,
"date": dt,
"timezone": Tweet.timezone,
"location": Tweet.location,
"tweet": Tweet.tweet,
"hashtags": Tweet.hashtags,
"user_id": Tweet.user_id,
"username": Tweet.username,
"day": day,
"hour": hour(Tweet.datetime),
"link": Tweet.link,
"retweet": Tweet.retweet,
"user_rt": Tweet.user_rt,
"essid": str(session),
"mentions": Tweet.mentions,
}
_blocks.append(_data)
|
def update(Tweet, session):
day = weekday(strftime("%A", localtime(Tweet.datetime)))
dt = "{} {}".format(Tweet.datestamp, Tweet.timestamp)
_data = {
"id": Tweet.id,
"date": dt,
"timezone": Tweet.timezone,
"location": Tweet.location,
"tweet": Tweet.tweet,
"hashtags": Tweet.hashtags,
"user_id": Tweet.user_id,
"username": Tweet.username,
"day": day,
"hour": hour(Tweet.datetime),
"link": Tweet.link,
"retweet": Tweet.retweet,
"user_rt": Tweet.user_rt,
"essid": str(session),
}
_blocks.append(_data)
|
https://github.com/twintproject/twint/issues/152
|
Traceback (most recent call last):
File "/path/to/my/script.py", line 21, in <module>
twint.run.Search(c)
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/run.py", line 25, in Search
run(search.Search(config).main())
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/run.py", line 5, in run
get_event_loop().run_until_complete(x)
File "/anaconda3/envs/twitter_scrape/lib/python3.6/asyncio/base_events.py", line 468, in run_until_complete
return future.result()
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/search.py", line 49, in main
await self.tweets()
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/search.py", line 37, in tweets
await output.Tweets(tweet, "", self.config, self.conn)
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/output.py", line 59, in Tweets
_output(tweet, output, config)
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/output.py", line 45, in _output
print(output)
UnicodeEncodeError: 'UCS-2' codec can't encode characters in position 389-389: Non-BMP character not supported in Tk
|
UnicodeEncodeError
|
def _output(obj, output, config):
if config.Output != None:
if config.Store_csv:
write.Csv(obj, config)
elif config.Store_json:
write.Json(obj, config)
else:
write.Text(output, config.Output)
if config.Pandas:
Pandas.update(obj, config.Essid)
if config.Elasticsearch:
if config.Store_object:
tweets_object.append(obj)
else:
print(output, end=".", flush=True)
else:
if config.Store_object:
tweets_object.append(obj)
else:
try:
print(output)
except UnicodeEncodeError:
pass
|
def _output(obj, output, config):
if config.Output != None:
if config.Store_csv:
write.Csv(obj, config)
elif config.Store_json:
write.Json(obj, config)
else:
write.Text(output, config.Output)
if config.Pandas:
Pandas.update(obj, config.Essid)
if config.Elasticsearch:
if config.Store_object:
tweets_object.append(obj)
else:
print(output, end=".", flush=True)
else:
if config.Store_object:
tweets_object.append(obj)
else:
print(output)
|
https://github.com/twintproject/twint/issues/152
|
Traceback (most recent call last):
File "/path/to/my/script.py", line 21, in <module>
twint.run.Search(c)
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/run.py", line 25, in Search
run(search.Search(config).main())
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/run.py", line 5, in run
get_event_loop().run_until_complete(x)
File "/anaconda3/envs/twitter_scrape/lib/python3.6/asyncio/base_events.py", line 468, in run_until_complete
return future.result()
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/search.py", line 49, in main
await self.tweets()
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/search.py", line 37, in tweets
await output.Tweets(tweet, "", self.config, self.conn)
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/output.py", line 59, in Tweets
_output(tweet, output, config)
File "/anaconda3/envs/twitter_scrape/lib/python3.6/site-packages/twint/output.py", line 45, in _output
print(output)
UnicodeEncodeError: 'UCS-2' codec can't encode characters in position 389-389: Non-BMP character not supported in Tk
|
UnicodeEncodeError
|
def __str__(self):
cls = self.obj.__class__
schema_path = ["{}.{}".format(cls.__module__, cls.__name__)]
schema_path.extend(self.schema_path)
schema_path = "->".join(
str(val)
for val in schema_path[:-1]
if val not in ("properties", "additionalProperties", "patternProperties")
)
return """Invalid specification
{}, validating {!r}
{}
""".format(schema_path, self.validator, self.message)
|
def __str__(self):
cls = self.obj.__class__
schema_path = ["{}.{}".format(cls.__module__, cls.__name__)]
schema_path.extend(self.schema_path)
schema_path = "->".join(
val
for val in schema_path[:-1]
if val not in ("properties", "additionalProperties", "patternProperties")
)
return """Invalid specification
{}, validating {!r}
{}
""".format(schema_path, self.validator, self.message)
|
https://github.com/altair-viz/altair/issues/1935
|
$ cat test.py
import pandas, altair
d = [{'WijkenEnBuurten': 'Nederland', 'Codering_3': 'NL00', 'Mannen_6': 8475102, 'Vrouwen_7': 8606405, 'SoortRegio_2': 'Land ', 'GeboorteRelatief_25': 9}, {'WijkenEnBuurten': 'Aa en Hunze', 'Codering_3': 'GM1680', 'Mannen_6': 12603, 'Vrouwen_7': 12683, 'SoortRegio_2': 'Gemeente ', 'GeboorteRelatief_25': 6}]
df = pandas.DataFrame(d)
a = altair.Data(df)
$ python ./test.py
Traceback (most recent call last):
File "./t_altair_schema.py", line 5, in <module>
a = altair.Data(df)
File "/home/paulm/.local/lib/python3.8/site-packages/altair/vegalite/v3/schema/core.py", line 3741, in __init__
super(Data, self).__init__(*args, **kwds)
File "/home/paulm/.local/lib/python3.8/site-packages/altair/utils/schemapi.py", line 154, in __init__
self.to_dict(validate=True)
File "/home/paulm/.local/lib/python3.8/site-packages/altair/utils/schemapi.py", line 302, in to_dict
raise SchemaValidationError(self, err)
altair.utils.schemapi.SchemaValidationError: <exception str() failed>
|
altair.utils.schemapi.SchemaValidationError
|
def __getattr__(self, attr):
# reminder: getattr is called after the normal lookups
if attr == "_kwds":
raise AttributeError()
if attr in self._kwds:
return self._kwds[attr]
else:
try:
_getattr = super(SchemaBase, self).__getattr__
except AttributeError:
_getattr = super(SchemaBase, self).__getattribute__
return _getattr(attr)
|
def __getattr__(self, attr):
# reminder: getattr is called after the normal lookups
if attr in self._kwds:
return self._kwds[attr]
else:
try:
_getattr = super(SchemaBase, self).__getattr__
except AttributeError:
_getattr = super(SchemaBase, self).__getattribute__
return _getattr(attr)
|
https://github.com/altair-viz/altair/issues/1681
|
(py36) C:\Develop\plab>python sandbox\test_altair_pickle.py
Traceback (most recent call last):
File "sandbox\test_altair_pickle.py", line 15, in <module>
pch = pickle.load(fid)
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
[Previous line repeated 330 more times]
RecursionError: maximum recursion depth exceeded while calling a Python object ```
|
RecursionError
|
def _subclasses(cls):
"""Breadth-first sequence of all classes which inherit from cls."""
seen = set()
current_set = {cls}
while current_set:
seen |= current_set
current_set = set.union(*(set(cls.__subclasses__()) for cls in current_set))
for cls in current_set - seen:
yield cls
|
def _subclasses(cls):
"""Breadth-first sequence of classes which inherit from cls."""
seen = set()
current_set = {cls}
while current_set:
seen |= current_set
current_set = set.union(*(set(cls.__subclasses__()) for cls in current_set))
for cls in current_set - seen:
yield cls
|
https://github.com/altair-viz/altair/issues/1681
|
(py36) C:\Develop\plab>python sandbox\test_altair_pickle.py
Traceback (most recent call last):
File "sandbox\test_altair_pickle.py", line 15, in <module>
pch = pickle.load(fid)
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
[Previous line repeated 330 more times]
RecursionError: maximum recursion depth exceeded while calling a Python object ```
|
RecursionError
|
def from_dict(self, dct, cls=None, schema=None, rootschema=None):
"""Construct an object from a dict representation"""
if (schema is None) == (cls is None):
raise ValueError("Must provide either cls or schema, but not both.")
if schema is None:
schema = schema or cls._schema
rootschema = rootschema or cls._rootschema
rootschema = rootschema or schema
def _passthrough(*args, **kwds):
return args[0] if args else kwds
if cls is None:
# If there are multiple matches, we use the last one in the dict.
# Our class dict is constructed breadth-first from top to bottom,
# so the last class that matches is the most specific.
matches = self.class_dict[self.hash_schema(schema)]
cls = matches[-1] if matches else _passthrough
schema = _resolve_references(schema, rootschema)
if "anyOf" in schema or "oneOf" in schema:
schemas = schema.get("anyOf", []) + schema.get("oneOf", [])
for possible_schema in schemas:
resolver = jsonschema.RefResolver.from_schema(rootschema)
try:
jsonschema.validate(dct, possible_schema, resolver=resolver)
except jsonschema.ValidationError:
continue
else:
return self.from_dict(
dct,
schema=possible_schema,
rootschema=rootschema,
)
if isinstance(dct, dict):
# TODO: handle schemas for additionalProperties/patternProperties
props = schema.get("properties", {})
kwds = {}
for key, val in dct.items():
if key in props:
val = self.from_dict(val, schema=props[key], rootschema=rootschema)
kwds[key] = val
return cls(**kwds)
elif isinstance(dct, list):
item_schema = schema.get("items", {})
dct = [
self.from_dict(val, schema=item_schema, rootschema=rootschema)
for val in dct
]
return cls(dct)
else:
return cls(dct)
|
def from_dict(self, dct, cls=None, schema=None, rootschema=None):
"""Construct an object from a dict representation"""
if (schema is None) == (cls is None):
raise ValueError("Must provide either cls or schema, but not both.")
if schema is None:
schema = schema or cls._schema
rootschema = rootschema or cls._rootschema
rootschema = rootschema or schema
def _passthrough(*args, **kwds):
return args[0] if args else kwds
if cls is None:
# TODO: do something more than simply selecting the last match?
matches = self.class_dict[self.hash_schema(schema)]
cls = matches[-1] if matches else _passthrough
schema = _resolve_references(schema, rootschema)
if "anyOf" in schema or "oneOf" in schema:
schemas = schema.get("anyOf", []) + schema.get("oneOf", [])
for possible_schema in schemas:
resolver = jsonschema.RefResolver.from_schema(rootschema)
try:
jsonschema.validate(dct, possible_schema, resolver=resolver)
except jsonschema.ValidationError:
continue
else:
return self.from_dict(
dct,
schema=possible_schema,
rootschema=rootschema,
)
if isinstance(dct, dict):
# TODO: handle schemas for additionalProperties/patternProperties
props = schema.get("properties", {})
kwds = {}
for key, val in dct.items():
if key in props:
val = self.from_dict(val, schema=props[key], rootschema=rootschema)
kwds[key] = val
return cls(**kwds)
elif isinstance(dct, list):
item_schema = schema.get("items", {})
dct = [
self.from_dict(val, schema=item_schema, rootschema=rootschema)
for val in dct
]
return cls(dct)
else:
return cls(dct)
|
https://github.com/altair-viz/altair/issues/1681
|
(py36) C:\Develop\plab>python sandbox\test_altair_pickle.py
Traceback (most recent call last):
File "sandbox\test_altair_pickle.py", line 15, in <module>
pch = pickle.load(fid)
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
File "C:\opt\Anaconda3\envs\py36\lib\site-packages\altair\utils\schemapi.py", line 213, in __getattr__
if attr in self._kwds:
[Previous line repeated 330 more times]
RecursionError: maximum recursion depth exceeded while calling a Python object ```
|
RecursionError
|
def transform_joinaggregate(self, joinaggregate=Undefined, groupby=Undefined, **kwargs):
"""
Add a JoinAggregateTransform to the schema.
Parameters
----------
joinaggregate : List(:class:`JoinAggregateFieldDef`)
The definition of the fields in the join aggregate, and what calculations to use.
groupby : List(string)
The data fields for partitioning the data objects into separate groups. If
unspecified, all data points will be in a single group.
**kwargs
joinaggregates can also be passed by keyword argument; see Examples.
Returns
-------
self : Chart object
returns chart to allow for chaining
Examples
--------
>>> import altair as alt
>>> chart = alt.Chart().transform_joinaggregate(x='sum(y)')
>>> chart.transform[0]
JoinAggregateTransform({
joinaggregate: [JoinAggregateFieldDef({
as: 'x',
field: 'y',
op: 'sum'
})]
})
See Also
--------
alt.JoinAggregateTransform : underlying transform object
"""
if joinaggregate is Undefined:
joinaggregate = []
for key, val in kwargs.items():
parsed = utils.parse_shorthand(val)
dct = {
"as": key,
"field": parsed.get("field", Undefined),
"op": parsed.get("aggregate", Undefined),
}
joinaggregate.append(core.JoinAggregateFieldDef(**dct))
return self._add_transform(
core.JoinAggregateTransform(joinaggregate=joinaggregate, groupby=groupby)
)
|
def transform_joinaggregate(self, joinaggregate=Undefined, groupby=Undefined, **kwargs):
"""
Add a JoinAggregateTransform to the schema.
Parameters
----------
joinaggregate : List(:class:`JoinAggregateFieldDef`)
The definition of the fields in the join aggregate, and what calculations to use.
groupby : List(string)
The data fields for partitioning the data objects into separate groups. If
unspecified, all data points will be in a single group.
**kwargs
joinaggregates can also be passed by keyword argument; see Examples.
Returns
-------
self : Chart object
returns chart to allow for chaining
Examples
--------
>>> import altair as alt
>>> chart = alt.Chart().transform_joinaggregate(x='sum(y)')
>>> chart.transform[0]
JoinAggregateTransform({
joinaggregate: [JoinAggregateFieldDef({
as: FieldName('x'),
field: FieldName('y'),
op: AggregateOp('sum')
})]
})
See Also
--------
alt.JoinAggregateTransform : underlying transform object
"""
if joinaggregate is Undefined:
joinaggregate = []
for key, val in kwargs.items():
parsed = utils.parse_shorthand(val)
dct = {
"as": key,
"field": parsed.get("field", Undefined),
"op": parsed.get("aggregate", Undefined),
}
joinaggregate.append(core.JoinAggregateFieldDef.from_dict(dct))
return self._add_transform(
core.JoinAggregateTransform(joinaggregate=joinaggregate, groupby=groupby)
)
|
https://github.com/altair-viz/altair/issues/1750
|
---------------------------------------------------------------------------
ValidationError Traceback (most recent call last)
<ipython-input-142-2bf583dd0be9> in <module>()
5 ).transform_joinaggregate(
6 group_count='count()',
----> 7 groupby=['group']
8 ).transform_calculate(
9 normalized_a="datum.a / datum.group_count",
~/.virtualenvs/simulate/lib/python3.6/site-packages/altair/vegalite/v3/api.py in transform_joinaggregate(self, joinaggregate, groupby, **kwargs)
929 'field': parsed.get('field', Undefined),
930 'op': parsed.get('aggregate', Undefined)}
--> 931 joinaggregate.append(core.JoinAggregateFieldDef.from_dict(dct))
932 return self._add_transform(core.JoinAggregateTransform(
933 joinaggregate=joinaggregate, groupby=groupby
~/.virtualenvs/simulate/lib/python3.6/site-packages/altair/utils/schemapi.py in from_dict(cls, dct, validate, _wrapper_classes)
366 """
367 if validate:
--> 368 cls.validate(dct)
369 if _wrapper_classes is None:
370 _wrapper_classes = cls._default_wrapper_classes()
~/.virtualenvs/simulate/lib/python3.6/site-packages/altair/utils/schemapi.py in validate(cls, instance, schema)
402 schema = cls._schema
403 resolver = jsonschema.RefResolver.from_schema(cls._rootschema or cls._schema)
--> 404 return jsonschema.validate(instance, schema, resolver=resolver)
405
406 @classmethod
~/.virtualenvs/simulate/lib/python3.6/site-packages/jsonschema/validators.py in validate(instance, schema, cls, *args, **kwargs)
897 error = exceptions.best_match(validator.iter_errors(instance))
898 if error is not None:
--> 899 raise error
900
901
ValidationError: Undefined is not of type 'string'
Failed validating 'type' in schema['properties']['field']:
{'type': 'string'}
On instance['field']:
Undefined
|
ValidationError
|
def spec_to_image_mimebundle(
spec,
format,
mode,
vega_version,
vegaembed_version,
vegalite_version=None,
driver_timeout=10,
):
"""Conver a vega/vega-lite specification to a PNG/SVG image
Parameters
----------
spec : dict
a dictionary representing a vega-lite plot spec
format : string {'png' | 'svg'}
the file format to be saved.
mode : string {'vega' | 'vega-lite'}
The rendering mode.
vega_version : string
For html output, the version of vega.js to use
vegalite_version : string
For html output, the version of vegalite.js to use
vegaembed_version : string
For html output, the version of vegaembed.js to use
driver_timeout : int (optional)
the number of seconds to wait for page load before raising an
error (default: 10)
Returns
-------
output : dict
a mime-bundle representing the image
Note
----
This requires the pillow, selenium, and chrome headless packages to be
installed.
"""
# TODO: allow package versions to be specified
# TODO: detect & use local Jupyter caches of JS packages?
if format not in ["png", "svg"]:
raise NotImplementedError("format must be 'svg' and 'png'")
if mode not in ["vega", "vega-lite"]:
raise ValueError("mode must be 'vega' or 'vega-lite'")
if mode == "vega-lite" and vegalite_version is None:
raise ValueError("must specify vega-lite version")
if webdriver is None:
raise ImportError(
"selenium package is required for saving chart as {0}".format(format)
)
if ChromeOptions is None:
raise ImportError(
"chromedriver is required for saving chart as {0}".format(format)
)
html = HTML_TEMPLATE.format(
vega_version=vega_version,
vegalite_version=vegalite_version,
vegaembed_version=vegaembed_version,
)
try:
chrome_options = ChromeOptions()
chrome_options.add_argument("--headless")
if os.geteuid() == 0:
chrome_options.add_argument("--no-sandbox")
driver = webdriver.Chrome(chrome_options=chrome_options)
driver.set_page_load_timeout(driver_timeout)
with temporary_filename(suffix=".html") as htmlfile:
with open(htmlfile, "w") as f:
f.write(html)
driver.get("file://" + htmlfile)
online = driver.execute_script("return navigator.onLine")
if not online:
raise ValueError(
"Internet connection required for saving chart as {0}".format(
format
)
)
render = driver.execute_async_script(EXTRACT_CODE[format], spec, mode)
finally:
driver.close()
if format == "png":
return {"image/png": base64.decodebytes(render.split(",", 1)[1].encode())}
elif format == "svg":
return {"image/svg+xml": render}
|
def spec_to_image_mimebundle(
spec,
format,
mode,
vega_version,
vegaembed_version,
vegalite_version=None,
driver_timeout=10,
):
"""Conver a vega/vega-lite specification to a PNG/SVG image
Parameters
----------
spec : dict
a dictionary representing a vega-lite plot spec
format : string {'png' | 'svg'}
the file format to be saved.
mode : string {'vega' | 'vega-lite'}
The rendering mode.
vega_version : string
For html output, the version of vega.js to use
vegalite_version : string
For html output, the version of vegalite.js to use
vegaembed_version : string
For html output, the version of vegaembed.js to use
driver_timeout : int (optional)
the number of seconds to wait for page load before raising an
error (default: 10)
Returns
-------
output : dict
a mime-bundle representing the image
Note
----
This requires the pillow, selenium, and chrome headless packages to be
installed.
"""
# TODO: allow package versions to be specified
# TODO: detect & use local Jupyter caches of JS packages?
if format not in ["png", "svg"]:
raise NotImplementedError("format must be 'svg' and 'png'")
if mode not in ["vega", "vega-lite"]:
raise ValueError("mode must be 'vega' or 'vega-lite'")
if mode == "vega-lite" and vegalite_version is None:
raise ValueError("must specify vega-lite version")
if webdriver is None:
raise ImportError(
"selenium package is required for saving chart as {0}".format(format)
)
if ChromeOptions is None:
raise ImportError(
"chromedriver is required for saving chart as {0}".format(format)
)
html = HTML_TEMPLATE.format(
vega_version=vega_version,
vegalite_version=vegalite_version,
vegaembed_version=vegaembed_version,
)
try:
chrome_options = ChromeOptions()
chrome_options.add_argument("--headless")
if os.geteuid() == 0:
chrome_options.add_argument("--no-sandbox")
driver = webdriver.Chrome(chrome_options=chrome_options)
driver.set_page_load_timeout(driver_timeout)
try:
fd, htmlfile = tempfile.mkstemp(suffix=".html", text=True)
with open(htmlfile, "w") as f:
f.write(html)
driver.get("file://" + htmlfile)
online = driver.execute_script("return navigator.onLine")
if not online:
raise ValueError(
"Internet connection required for saving chart as {0}".format(
format
)
)
render = driver.execute_async_script(EXTRACT_CODE[format], spec, mode)
finally:
os.remove(htmlfile)
finally:
driver.close()
if format == "png":
return {"image/png": base64.decodebytes(render.split(",", 1)[1].encode())}
elif format == "svg":
return {"image/svg+xml": render}
|
https://github.com/altair-viz/altair/issues/649
|
---------------------------------------------------------------------------
PermissionError Traceback (most recent call last)
<ipython-input-16-c16ecf6573c1> in <module>()
----> 1 chart.savechart('test.png')
G:\Software\Anaconda2\envs\py36\lib\site-packages\altair\vegalite\v2\api.py in savechart(self, fp, format, **kwargs)
331 utils.write_file_or_filename(fp, spec_html, mode='w')
332 elif format in ['png', 'svg']:
--> 333 utils.save_spec(self.to_dict(), fp, format=format, **kwargs)
334 else:
335 raise ValueError("unrecognized format: '{0}'".format(format))
G:\Software\Anaconda2\envs\py36\lib\site-packages\altair\utils\headless.py in save_spec(spec, fp, mode, format, driver_timeout)
136 spec, mode)
137 finally:
--> 138 os.remove(htmlfile)
139 finally:
140 driver.close()
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\PAGPI_~1\\AppData\\Local\\Temp\\tmpbyp9uhvp.html'
|
PermissionError
|
def spec_to_image_mimebundle(
spec,
format,
mode,
vega_version,
vegaembed_version,
vegalite_version=None,
driver_timeout=10,
):
"""Conver a vega/vega-lite specification to a PNG/SVG image
Parameters
----------
spec : dict
a dictionary representing a vega-lite plot spec
format : string {'png' | 'svg'}
the file format to be saved.
mode : string {'vega' | 'vega-lite'}
The rendering mode.
vega_version : string
For html output, the version of vega.js to use
vegalite_version : string
For html output, the version of vegalite.js to use
vegaembed_version : string
For html output, the version of vegaembed.js to use
driver_timeout : int (optional)
the number of seconds to wait for page load before raising an
error (default: 10)
Returns
-------
output : dict
a mime-bundle representing the image
Note
----
This requires the pillow, selenium, and chrome headless packages to be
installed.
"""
# TODO: allow package versions to be specified
# TODO: detect & use local Jupyter caches of JS packages?
if format not in ["png", "svg"]:
raise NotImplementedError("format must be 'svg' and 'png'")
if mode not in ["vega", "vega-lite"]:
raise ValueError("mode must be 'vega' or 'vega-lite'")
if mode == "vega-lite" and vegalite_version is None:
raise ValueError("must specify vega-lite version")
if webdriver is None:
raise ImportError(
"selenium package is required for saving chart as {0}".format(format)
)
if ChromeOptions is None:
raise ImportError(
"chromedriver is required for saving chart as {0}".format(format)
)
html = HTML_TEMPLATE.format(
vega_version=vega_version,
vegalite_version=vegalite_version,
vegaembed_version=vegaembed_version,
)
chrome_options = ChromeOptions()
chrome_options.add_argument("--headless")
# for linux/osx root user, need to add --no-sandbox option.
# since geteuid doesn't exist on windows, we don't check it
if hasattr(os, "geteuid") and (os.geteuid() == 0):
chrome_options.add_argument("--no-sandbox")
driver = webdriver.Chrome(chrome_options=chrome_options)
try:
driver.set_page_load_timeout(driver_timeout)
with temporary_filename(suffix=".html") as htmlfile:
with open(htmlfile, "w") as f:
f.write(html)
driver.get("file://" + htmlfile)
online = driver.execute_script("return navigator.onLine")
if not online:
raise ValueError(
"Internet connection required for saving chart as {0}".format(
format
)
)
render = driver.execute_async_script(EXTRACT_CODE[format], spec, mode)
finally:
driver.close()
if format == "png":
return {"image/png": base64.decodebytes(render.split(",", 1)[1].encode())}
elif format == "svg":
return {"image/svg+xml": render}
|
def spec_to_image_mimebundle(
spec,
format,
mode,
vega_version,
vegaembed_version,
vegalite_version=None,
driver_timeout=10,
):
"""Conver a vega/vega-lite specification to a PNG/SVG image
Parameters
----------
spec : dict
a dictionary representing a vega-lite plot spec
format : string {'png' | 'svg'}
the file format to be saved.
mode : string {'vega' | 'vega-lite'}
The rendering mode.
vega_version : string
For html output, the version of vega.js to use
vegalite_version : string
For html output, the version of vegalite.js to use
vegaembed_version : string
For html output, the version of vegaembed.js to use
driver_timeout : int (optional)
the number of seconds to wait for page load before raising an
error (default: 10)
Returns
-------
output : dict
a mime-bundle representing the image
Note
----
This requires the pillow, selenium, and chrome headless packages to be
installed.
"""
# TODO: allow package versions to be specified
# TODO: detect & use local Jupyter caches of JS packages?
if format not in ["png", "svg"]:
raise NotImplementedError("format must be 'svg' and 'png'")
if mode not in ["vega", "vega-lite"]:
raise ValueError("mode must be 'vega' or 'vega-lite'")
if mode == "vega-lite" and vegalite_version is None:
raise ValueError("must specify vega-lite version")
if webdriver is None:
raise ImportError(
"selenium package is required for saving chart as {0}".format(format)
)
if ChromeOptions is None:
raise ImportError(
"chromedriver is required for saving chart as {0}".format(format)
)
html = HTML_TEMPLATE.format(
vega_version=vega_version,
vegalite_version=vegalite_version,
vegaembed_version=vegaembed_version,
)
try:
chrome_options = ChromeOptions()
chrome_options.add_argument("--headless")
if os.geteuid() == 0:
chrome_options.add_argument("--no-sandbox")
driver = webdriver.Chrome(chrome_options=chrome_options)
driver.set_page_load_timeout(driver_timeout)
with temporary_filename(suffix=".html") as htmlfile:
with open(htmlfile, "w") as f:
f.write(html)
driver.get("file://" + htmlfile)
online = driver.execute_script("return navigator.onLine")
if not online:
raise ValueError(
"Internet connection required for saving chart as {0}".format(
format
)
)
render = driver.execute_async_script(EXTRACT_CODE[format], spec, mode)
finally:
driver.close()
if format == "png":
return {"image/png": base64.decodebytes(render.split(",", 1)[1].encode())}
elif format == "svg":
return {"image/svg+xml": render}
|
https://github.com/altair-viz/altair/issues/649
|
---------------------------------------------------------------------------
PermissionError Traceback (most recent call last)
<ipython-input-16-c16ecf6573c1> in <module>()
----> 1 chart.savechart('test.png')
G:\Software\Anaconda2\envs\py36\lib\site-packages\altair\vegalite\v2\api.py in savechart(self, fp, format, **kwargs)
331 utils.write_file_or_filename(fp, spec_html, mode='w')
332 elif format in ['png', 'svg']:
--> 333 utils.save_spec(self.to_dict(), fp, format=format, **kwargs)
334 else:
335 raise ValueError("unrecognized format: '{0}'".format(format))
G:\Software\Anaconda2\envs\py36\lib\site-packages\altair\utils\headless.py in save_spec(spec, fp, mode, format, driver_timeout)
136 spec, mode)
137 finally:
--> 138 os.remove(htmlfile)
139 finally:
140 driver.close()
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\PAGPI_~1\\AppData\\Local\\Temp\\tmpbyp9uhvp.html'
|
PermissionError
|
async def async_setup_frontend():
"""Configure the HACS frontend elements."""
hacs = get_hacs()
hacs.log.info("Setup task %s", HacsSetupTask.FRONTEND)
# Custom view
hacs.hass.http.register_view(HacsFrontend())
# Custom iconset
if "frontend_extra_module_url" not in hacs.hass.data:
hacs.hass.data["frontend_extra_module_url"] = set()
hacs.hass.data["frontend_extra_module_url"].add("/hacsfiles/iconset.js")
hacs.frontend.version_running = FE_VERSION
hacs.frontend.version_expected = await hacs.hass.async_add_executor_job(
get_frontend_version
)
# Add to sidepanel
if "hacs" not in hacs.hass.data.get("frontend_panels", {}):
custom_panel_config = {
"name": "hacs-frontend",
"embed_iframe": True,
"trust_external": False,
"js_url": "/hacsfiles/frontend/entrypoint.js",
}
config = {}
config["_panel_custom"] = custom_panel_config
hacs.hass.components.frontend.async_register_built_in_panel(
component_name="custom",
sidebar_title=hacs.configuration.sidepanel_title,
sidebar_icon=hacs.configuration.sidepanel_icon,
frontend_url_path="hacs",
config=config,
require_admin=True,
)
|
async def async_setup_frontend():
"""Configure the HACS frontend elements."""
hacs = get_hacs()
hacs.log.info("Setup task %s", HacsSetupTask.FRONTEND)
# Custom view
hacs.hass.http.register_view(HacsFrontend())
# Custom iconset
if "frontend_extra_module_url" not in hacs.hass.data:
hacs.hass.data["frontend_extra_module_url"] = set()
hacs.hass.data["frontend_extra_module_url"].add("/hacsfiles/iconset.js")
hacs.frontend.version_running = FE_VERSION
hacs.frontend.version_expected = await hacs.hass.async_add_executor_job(
get_frontend_version
)
# Add to sidepanel
custom_panel_config = {
"name": "hacs-frontend",
"embed_iframe": True,
"trust_external": False,
"js_url": "/hacsfiles/frontend/entrypoint.js",
}
config = {}
config["_panel_custom"] = custom_panel_config
hacs.hass.components.frontend.async_register_built_in_panel(
component_name="custom",
sidebar_title=hacs.configuration.sidepanel_title,
sidebar_icon=hacs.configuration.sidepanel_icon,
frontend_url_path="hacs",
config=config,
require_admin=True,
)
|
https://github.com/hacs/integration/issues/1605
|
2020-10-27 16:42:22 ERROR (MainThread) [homeassistant.config_entries] Error setting up entry for hacs
Traceback (most recent call last):
File "/usr/src/homeassistant/homeassistant/config_entries.py", line 234, in async_setup
result = await component.async_setup_entry(hass, self) # type: ignore
File "/config/custom_components/hacs/__init__.py", line 30, in async_setup_entry
return await hacs_ui_setup(hass, config_entry)
File "/config/custom_components/hacs/operational/setup.py", line 63, in async_setup_entry
return await async_startup_wrapper_for_config_entry()
File "/config/custom_components/hacs/operational/setup.py", line 88, in async_startup_wrapper_for_config_entry
startup_result = await async_hacs_startup()
File "/config/custom_components/hacs/operational/setup.py", line 133, in async_hacs_startup
await async_setup_frontend()
File "/config/custom_components/hacs/operational/setup_actions/frontend.py", line 38, in async_setup_frontend
hacs.hass.components.frontend.async_register_built_in_panel(
File "/usr/src/homeassistant/homeassistant/components/frontend/__init__.py", line 196, in async_register_built_in_panel
raise ValueError(f"Overwriting panel {panel.frontend_url_path}")
ValueError: Overwriting panel hacs
|
ValueError
|
def create_window(
title,
url=None,
js_api=None,
width=800,
height=600,
resizable=True,
fullscreen=False,
min_size=(200, 100),
strings={},
confirm_quit=False,
background_color="#FFFFFF",
text_select=False,
debug=False,
):
"""
Create a web view window using a native GUI. The execution blocks after this function is invoked, so other
program logic must be executed in a separate thread.
:param title: Window title
:param url: URL to load
:param width: window width. Default is 800px
:param height:window height. Default is 600px
:param resizable True if window can be resized, False otherwise. Default is True
:param fullscreen: True if start in fullscreen mode. Default is False
:param min_size: a (width, height) tuple that specifies a minimum window size. Default is 200x100
:param strings: a dictionary with localized strings
:param confirm_quit: Display a quit confirmation dialog. Default is False
:param background_color: Background color as a hex string that is displayed before the content of webview is loaded. Default is white.
:param text_select: Allow text selection on page. Default is False.
:return: The uid of the created window.
"""
valid_color = r"^#(?:[0-9a-fA-F]{3}){1,2}$"
if not re.match(valid_color, background_color):
raise ValueError(
"{0} is not a valid hex triplet color".format(background_color)
)
# Check if starting up from main thread; if not, wait; finally raise exception
if current_thread().name == "MainThread":
uid = "master"
if not _initialized:
_initialize_imports()
localization.update(strings)
else:
uid = "child_" + uuid4().hex[:8]
if not _webview_ready.wait(5):
raise Exception(
"Call create_window from the main thread first, and then from subthreads"
)
_webview_ready.clear() # Make API calls wait while the new window is created
gui.create_window(
uid,
make_unicode(title),
transform_url(url),
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
_webview_ready,
)
return uid
|
def create_window(
title,
url=None,
js_api=None,
width=800,
height=600,
resizable=True,
fullscreen=False,
min_size=(200, 100),
strings={},
confirm_quit=False,
background_color="#FFFFFF",
text_select=False,
debug=False,
):
"""
Create a web view window using a native GUI. The execution blocks after this function is invoked, so other
program logic must be executed in a separate thread.
:param title: Window title
:param url: URL to load
:param width: window width. Default is 800px
:param height:window height. Default is 600px
:param resizable True if window can be resized, False otherwise. Default is True
:param fullscreen: True if start in fullscreen mode. Default is False
:param min_size: a (width, height) tuple that specifies a minimum window size. Default is 200x100
:param strings: a dictionary with localized strings
:param confirm_quit: Display a quit confirmation dialog. Default is False
:param background_color: Background color as a hex string that is displayed before the content of webview is loaded. Default is white.
:param text_select: Allow text selection on page. Default is False.
:return: The uid of the created window.
"""
uid = "child_" + uuid4().hex[:8]
valid_color = r"^#(?:[0-9a-fA-F]{3}){1,2}$"
if not re.match(valid_color, background_color):
raise ValueError(
"{0} is not a valid hex triplet color".format(background_color)
)
if not _initialized:
# Check if starting up from main thread; if not, wait; finally raise exception
if current_thread().name != "MainThread":
if not _webview_ready.wait(5):
raise Exception(
"Call create_window from the main thread first, and then from subthreads"
)
else:
_initialize_imports()
localization.update(strings)
uid = "master"
_webview_ready.clear() # Make API calls wait while the new window is created
gui.create_window(
uid,
make_unicode(title),
transform_url(url),
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
_webview_ready,
)
return uid
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def windowWillClose_(self, notification):
# Delete the closed instance from the dict
i = BrowserView.get_instance("window", notification.object())
del BrowserView.instances[i.uid]
if BrowserView.instances == {}:
AppHelper.callAfter(BrowserView.app.stop_, self)
|
def windowWillClose_(self, notification):
# Delete the closed instance from the dict
i = BrowserView.get_instance("window", notification.object())
del BrowserView.instances[i.uid]
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def webView_didFinishLoadForFrame_(self, webview, frame):
# Add the webview to the window if it's not yet the contentView
i = BrowserView.get_instance("webkit", webview)
if i and not webview.window():
i.window.setContentView_(webview)
i.window.makeFirstResponder_(webview)
if i.js_bridge:
i._set_js_api()
if not i.text_select:
i.webkit.windowScriptObject().evaluateWebScript_(disable_text_select)
i.loaded.set()
|
def webView_didFinishLoadForFrame_(self, webview, frame):
# Add the webview to the window if it's not yet the contentView
i = BrowserView.get_instance("webkit", webview)
if not webview.window():
i.window.setContentView_(webview)
i.window.makeFirstResponder_(webview)
if i.js_bridge:
i._set_js_api()
if not i.text_select:
i.webkit.windowScriptObject().evaluateWebScript_(disable_text_select)
i.loaded.set()
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def performKeyEquivalent_(self, theEvent):
"""
Handle common hotkey shortcuts as copy/cut/paste/undo/select all/quit
:param theEvent:
:return:
"""
if (
theEvent.type() == AppKit.NSKeyDown
and theEvent.modifierFlags() & AppKit.NSCommandKeyMask
):
responder = self.window().firstResponder()
keyCode = theEvent.keyCode()
if responder != None:
handled = False
range_ = responder.selectedRange()
hasSelectedText = len(range_) > 0
if keyCode == 7 and hasSelectedText: # cut
responder.cut_(self)
handled = True
elif keyCode == 8 and hasSelectedText: # copy
responder.copy_(self)
handled = True
elif keyCode == 9: # paste
responder.paste_(self)
handled = True
elif keyCode == 0: # select all
responder.selectAll_(self)
handled = True
elif keyCode == 6: # undo
if responder.undoManager().canUndo():
responder.undoManager().undo()
handled = True
elif keyCode == 12: # quit
BrowserView.app.stop_(self)
return handled
|
def performKeyEquivalent_(self, theEvent):
"""
Handle common hotkey shortcuts as copy/cut/paste/undo/select all/quit
:param theEvent:
:return:
"""
if (
theEvent.type() == AppKit.NSKeyDown
and theEvent.modifierFlags() & AppKit.NSCommandKeyMask
):
responder = self.window().firstResponder()
keyCode = theEvent.keyCode()
if responder != None:
handled = False
range_ = responder.selectedRange()
hasSelectedText = len(range_) > 0
if keyCode == 7 and hasSelectedText: # cut
responder.cut_(self)
handled = True
elif keyCode == 8 and hasSelectedText: # copy
responder.copy_(self)
handled = True
elif keyCode == 9: # paste
responder.paste_(self)
handled = True
elif keyCode == 0: # select all
responder.selectAll_(self)
handled = True
elif keyCode == 6: # undo
if responder.undoManager().canUndo():
responder.undoManager().undo()
handled = True
elif keyCode == 12: # quit
BrowserView.app.terminate_(self)
return handled
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def __init__(
self,
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
):
BrowserView.instances[uid] = self
self.uid = uid
if debug:
BrowserView.debug = debug
BrowserView._set_debugging()
self.js_bridge = None
self._file_name = None
self._file_name_semaphore = Semaphore(0)
self._current_url_semaphore = Semaphore(0)
self.webview_ready = webview_ready
self.loaded = Event()
self.confirm_quit = confirm_quit
self.title = title
self.text_select = text_select
self.is_fullscreen = False
rect = AppKit.NSMakeRect(0.0, 0.0, width, height)
window_mask = (
AppKit.NSTitledWindowMask
| AppKit.NSClosableWindowMask
| AppKit.NSMiniaturizableWindowMask
)
if resizable:
window_mask = window_mask | AppKit.NSResizableWindowMask
# The allocated resources are retained because we would explicitly delete
# this instance when its window is closed
self.window = (
AppKit.NSWindow.alloc()
.initWithContentRect_styleMask_backing_defer_(
rect, window_mask, AppKit.NSBackingStoreBuffered, False
)
.retain()
)
self.window.setTitle_(title)
self.window.setBackgroundColor_(BrowserView.nscolor_from_hex(background_color))
self.window.setMinSize_(AppKit.NSSize(min_size[0], min_size[1]))
self.window.setAnimationBehavior_(AppKit.NSWindowAnimationBehaviorDocumentWindow)
BrowserView.cascade_loc = self.window.cascadeTopLeftFromPoint_(
BrowserView.cascade_loc
)
# Set the titlebar color (so that it does not change with the window color)
self.window.contentView().superview().subviews().lastObject().setBackgroundColor_(
AppKit.NSColor.windowBackgroundColor()
)
self.webkit = BrowserView.WebKitHost.alloc().initWithFrame_(rect).retain()
self._browserDelegate = BrowserView.BrowserDelegate.alloc().init().retain()
self._windowDelegate = BrowserView.WindowDelegate.alloc().init().retain()
self._appDelegate = BrowserView.AppDelegate.alloc().init().retain()
self.webkit.setUIDelegate_(self._browserDelegate)
self.webkit.setFrameLoadDelegate_(self._browserDelegate)
self.webkit.setPolicyDelegate_(self._browserDelegate)
self.window.setDelegate_(self._windowDelegate)
BrowserView.app.setDelegate_(self._appDelegate)
if url:
self.url = url
self.load_url(url)
else:
self.loaded.set()
if js_api:
self.js_bridge = BrowserView.JSBridge.alloc().initWithObject_(js_api)
if fullscreen:
self.toggle_fullscreen()
|
def __init__(
self,
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
):
BrowserView.instances[uid] = self
self.uid = uid
if debug:
BrowserView.debug = debug
BrowserView._set_debugging()
self.js_bridge = None
self._file_name = None
self._file_name_semaphore = Semaphore(0)
self._current_url_semaphore = Semaphore(0)
self.webview_ready = webview_ready
self.loaded = Event()
self.confirm_quit = confirm_quit
self.title = title
self.text_select = text_select
self.is_fullscreen = False
rect = AppKit.NSMakeRect(0.0, 0.0, width, height)
window_mask = (
AppKit.NSTitledWindowMask
| AppKit.NSClosableWindowMask
| AppKit.NSMiniaturizableWindowMask
)
if resizable:
window_mask = window_mask | AppKit.NSResizableWindowMask
# The allocated resources are retained because we would explicitly delete
# this instance when its window is closed
self.window = (
AppKit.NSWindow.alloc()
.initWithContentRect_styleMask_backing_defer_(
rect, window_mask, AppKit.NSBackingStoreBuffered, False
)
.retain()
)
self.window.setTitle_(title)
self.window.setBackgroundColor_(BrowserView.nscolor_from_hex(background_color))
self.window.setMinSize_(AppKit.NSSize(min_size[0], min_size[1]))
BrowserView.cascade_loc = self.window.cascadeTopLeftFromPoint_(
BrowserView.cascade_loc
)
# Set the titlebar color (so that it does not change with the window color)
self.window.contentView().superview().subviews().lastObject().setBackgroundColor_(
AppKit.NSColor.windowBackgroundColor()
)
self.webkit = BrowserView.WebKitHost.alloc().initWithFrame_(rect).retain()
self._browserDelegate = BrowserView.BrowserDelegate.alloc().init().retain()
self._windowDelegate = BrowserView.WindowDelegate.alloc().init().retain()
self._appDelegate = BrowserView.AppDelegate.alloc().init().retain()
self.webkit.setUIDelegate_(self._browserDelegate)
self.webkit.setFrameLoadDelegate_(self._browserDelegate)
self.webkit.setPolicyDelegate_(self._browserDelegate)
self.window.setDelegate_(self._windowDelegate)
BrowserView.app.setDelegate_(self._appDelegate)
if url:
self.url = url
self.load_url(url)
else:
self.loaded.set()
if js_api:
self.js_bridge = BrowserView.JSBridge.alloc().initWithObject_(js_api)
if fullscreen:
self.toggle_fullscreen()
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def on_inspect_webview(self, inspector, webview):
title = "Web Inspector - {}".format(self.window.get_title())
uid = self.uid + "-inspector"
inspector = BrowserView(
uid,
title,
"",
700,
500,
True,
False,
(300, 200),
False,
"#fff",
False,
None,
True,
self.webview_ready,
)
inspector.show()
return inspector.webview
|
def on_inspect_webview(self, inspector, webview):
title = "Web Inspector - {}".format(self.window.get_title())
uid = self.uid + "-inspector"
inspector = BrowserView(
uid,
title,
"",
700,
500,
True,
False,
(300, 200),
False,
"#fff",
False,
None,
self.webview_ready,
)
inspector.show()
return inspector.webview
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def evaluate_js(self, script):
def _evaluate_js():
self.webview.execute_script(code)
result_semaphore.release()
self.eval_js_lock.acquire()
result_semaphore = Semaphore(0)
self.js_result_semaphores.append(result_semaphore)
# Backup the doc title and store the result in it with a custom prefix
unique_id = uuid1().hex
code = "window.oldTitle{0} = document.title; document.title = {1};".format(
unique_id, script
)
self.load_event.wait()
glib.idle_add(_evaluate_js)
result_semaphore.acquire()
if not gtk.main_level():
# Webview has been closed, don't proceed
return None
result = self.webview.get_title()
result = (
None
if result == "undefined" or result == "null" or result is None
else result
if result == ""
else json.loads(result)
)
# Restore document title and return
code = "document.title = window.oldTitle{0}".format(unique_id)
glib.idle_add(_evaluate_js)
self.js_result_semaphores.remove(result_semaphore)
self.eval_js_lock.release()
return result
|
def evaluate_js(self, script):
def _evaluate_js():
self.webview.execute_script(code)
result_semaphore.release()
self.eval_js_lock.acquire()
result_semaphore = Semaphore(0)
self.js_result_semaphores.append(result_semaphore)
# Backup the doc title and store the result in it with a custom prefix
unique_id = uuid1().hex
code = "window.oldTitle{0} = document.title; document.title = {1};".format(
unique_id, script
)
self.load_event.wait()
glib.idle_add(_evaluate_js)
result_semaphore.acquire()
if not gtk.main_level():
# Webview has been closed, don't proceed
return None
result = self.webview.get_title()
result = (
None
if result == "undefined" or result == "null"
else result
if result == ""
else json.loads(result)
)
# Restore document title and return
code = "document.title = window.oldTitle{0}".format(unique_id)
glib.idle_add(_evaluate_js)
self.js_result_semaphores.remove(result_semaphore)
self.eval_js_lock.release()
return result
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def show_inspector(self):
uid = self.parent().uid + "-inspector"
try:
# If inspector already exists, bring it to the front
BrowserView.instances[uid].raise_()
BrowserView.instances[uid].activateWindow()
except KeyError:
title = "Web Inspector - {}".format(self.parent().title)
url = "http://localhost:{}".format(BrowserView.inspector_port)
inspector = BrowserView(
uid,
title,
url,
700,
500,
True,
False,
(300, 200),
False,
"#fff",
False,
None,
True,
self.parent().webview_ready,
)
inspector.show()
|
def show_inspector(self):
uid = self.parent().uid + "-inspector"
try:
# If inspector already exists, bring it to the front
BrowserView.instances[uid].raise_()
BrowserView.instances[uid].activateWindow()
except KeyError:
title = "Web Inspector - {}".format(self.parent().title)
url = "http://localhost:{}".format(BrowserView.inspector_port)
inspector = BrowserView(
uid,
title,
url,
700,
500,
True,
False,
(300, 200),
False,
"#fff",
False,
None,
self.parent().webview_ready,
)
inspector.show()
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def closeEvent(self, event):
if self.confirm_quit:
reply = QMessageBox.question(
self,
self.title,
localization["global.quitConfirmation"],
QMessageBox.Yes,
QMessageBox.No,
)
if reply == QMessageBox.No:
event.ignore()
return
event.accept()
del BrowserView.instances[self.uid]
try: # Close inspector if open
BrowserView.instances[self.uid + "-inspector"].close()
del BrowserView.instances[self.uid + "-inspector"]
except KeyError:
pass
if len(BrowserView.instances) == 0:
_app.exit()
|
def closeEvent(self, event):
if self.confirm_quit:
reply = QMessageBox.question(
self,
self.title,
localization["global.quitConfirmation"],
QMessageBox.Yes,
QMessageBox.No,
)
if reply == QMessageBox.No:
event.ignore()
return
event.accept()
del BrowserView.instances[self.uid]
try: # Close inpsector if open
BrowserView.instances[self.uid + "-inspector"].close()
del BrowserView.instances[self.uid + "-inspector"]
except KeyError:
pass
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def create_window(
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
):
global _app
_app = QApplication.instance() or QApplication([])
def _create():
browser = BrowserView(
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
)
browser.show()
if uid == "master":
_create()
_app.exec_()
else:
i = list(BrowserView.instances.values())[0] # arbitrary instance
i.create_window_trigger.emit(_create)
|
def create_window(
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
):
app = QApplication.instance() or QApplication([])
def _create():
browser = BrowserView(
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
)
browser.show()
if uid == "master":
_create()
app.exec_()
else:
i = list(BrowserView.instances.values())[0] # arbitrary instance
i.create_window_trigger.emit(_create)
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def create_window(
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
):
def create():
window = BrowserView.BrowserForm(
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
)
BrowserView.instances[uid] = window
window.Show()
if uid == "master":
app.Run()
webview_ready.clear()
app = WinForms.Application
if uid == "master":
set_ie_mode()
if sys.getwindowsversion().major >= 6:
windll.user32.SetProcessDPIAware()
app.EnableVisualStyles()
app.SetCompatibleTextRenderingDefault(False)
thread = Thread(ThreadStart(create))
thread.SetApartmentState(ApartmentState.STA)
thread.Start()
thread.Join()
else:
i = list(BrowserView.instances.values())[0] # arbitrary instance
i.Invoke(Func[Type](create))
|
def create_window(
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
):
def create():
window = BrowserView.BrowserForm(
uid,
title,
url,
width,
height,
resizable,
fullscreen,
min_size,
confirm_quit,
background_color,
debug,
js_api,
text_select,
webview_ready,
)
BrowserView.instances[uid] = window
window.Show()
if uid == "master":
app.Run()
webview_ready.clear()
app = WinForms.Application
if uid == "master":
set_ie_mode()
if sys.getwindowsversion().major >= 6:
windll.user32.SetProcessDPIAware()
app.EnableVisualStyles()
app.SetCompatibleTextRenderingDefault(False)
thread = Thread(ThreadStart(create))
thread.SetApartmentState(ApartmentState.STA)
thread.Start()
thread.Join()
else:
BrowserView.instances["master"].Invoke(Func[Type](create))
|
https://github.com/r0x0r/pywebview/issues/229
|
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Program Files\Python36\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Program Files\Python36\lib\threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "ui_pywebview.py", line 23, in create_second_window
second_window = webview.create_window("Window 2", os.path.abspath("web\\window2.html"), js_api=SecondWindowApi)
File "C:\Program Files\Python36\lib\site-packages\webview\__init__.py", line 183, in create_window
background_color, debug, js_api, text_select, _webview_ready)
File "C:\Program Files\Python36\lib\site-packages\webview\winforms.py", line 252, in create_window
BrowserView.instances['master'].Invoke(Func[Type](create))
KeyError: 'master'
|
KeyError
|
def _switch(self, chara, charb):
if self._isdigit(chara):
return 0, not self._isdigit(charb)
if self._isletter(chara):
return 1, not self._isletter(charb)
return 2, self._isdigit(charb) or self._isletter(charb)
|
def _switch(self, chara, charb):
if self._isdigit(chara):
return 0, not self._isdigit(charb)
if self._isletter(chara):
return 1, not self._isletter(charb)
if self._isnonword(chara):
return 2, not self._isnonword(charb)
return "", True
|
https://github.com/scrapinghub/dateparser/issues/621
|
dateparser.parse('Oct 1 2018 4:40 PM EST —')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "dateparser/conf.py", line 82, in wrapper
return f(*args, **kwargs)
File "dateparser/__init__.py", line 53, in parse
data = parser.get_date_data(date_string, date_formats)
File "dateparser/date.py", line 417, in get_date_data
locale, date_string, date_formats, settings=self._settings)
File "dateparser/date.py", line 189, in parse
return instance._parse()
File "dateparser/date.py", line 199, in _parse
date_obj = parser()
File "dateparser/date.py", line 222, in _try_parser
self._get_translated_date(), settings=self._settings)
File "dateparser/conf.py", line 82, in wrapper
return f(*args, **kwargs)
File "dateparser/date_parser.py", line 26, in parse
date_obj, period = parse(date_string, settings=settings)
File "dateparser/parser.py", line 70, in parse
raise exceptions.pop(-1)
File "dateparser/parser.py", line 64, in parse
res = parser(datestring, settings)
File "dateparser/parser.py", line 446, in parse
po = cls(tokens.tokenize(), settings)
File "dateparser/parser.py", line 192, in __init__
self.filtered_tokens = [t for t in self.tokens if t[1] <= 1]
File "dateparser/parser.py", line 192, in <listcomp>
self.filtered_tokens = [t for t in self.tokens if t[1] <= 1]
TypeError: '<=' not supported between instances of 'str' and 'int'
|
TypeError
|
def __init__(self, tokens, settings):
self.settings = settings
self.tokens = list(tokens)
self.filtered_tokens = [t for t in self.tokens if t[1] <= 1]
self.unset_tokens = []
self.day = None
self.month = None
self.year = None
self.time = None
self.auto_order = []
self._token_day = None
self._token_month = None
self._token_year = None
self._token_time = None
self.ordered_num_directives = OrderedDict(
(k, self.num_directives[k])
for k in (resolve_date_order(settings.DATE_ORDER, lst=True))
)
skip_index = []
skip_component = None
for index, token_type in enumerate(self.filtered_tokens):
if index in skip_index:
continue
token, type = token_type
if token in settings.SKIP_TOKENS_PARSER:
continue
if self.time is None:
try:
microsecond = MICROSECOND.search(
self.filtered_tokens[index + 1][0]
).group()
_is_after_time_token = token.index(":")
_is_after_period = self.tokens[self.tokens.index((token, 0)) + 1][
0
].index(".")
except:
microsecond = None
if microsecond:
mindex = index + 2
else:
mindex = index + 1
try:
meridian = MERIDIAN.search(self.filtered_tokens[mindex][0]).group()
except:
meridian = None
if any([":" in token, meridian, microsecond]):
if meridian and not microsecond:
self._token_time = "%s %s" % (token, meridian)
skip_index.append(mindex)
elif microsecond and not meridian:
self._token_time = "%s.%s" % (token, microsecond)
skip_index.append(index + 1)
elif meridian and microsecond:
self._token_time = "%s.%s %s" % (token, microsecond, meridian)
skip_index.append(index + 1)
skip_index.append(mindex)
else:
self._token_time = token
self.time = lambda: time_parser(self._token_time)
continue
results = self._parse(
type, token, settings.FUZZY, skip_component=skip_component
)
for res in results:
if len(token) == 4 and res[0] == "year":
skip_component = "year"
setattr(self, *res)
known, unknown = get_unresolved_attrs(self)
params = {}
for attr in known:
params.update({attr: getattr(self, attr)})
for attr in unknown:
for token, type, _ in self.unset_tokens:
if type == 0:
params.update({attr: int(token)})
setattr(self, "_token_%s" % attr, token)
setattr(self, attr, int(token))
|
def __init__(self, tokens, settings):
self.settings = settings
self.tokens = list(tokens)
self.filtered_tokens = [t for t in self.tokens if t[1] <= 1]
self.unset_tokens = []
self.day = None
self.month = None
self.year = None
self.time = None
self.auto_order = []
self._token_day = None
self._token_month = None
self._token_year = None
self._token_time = None
self.ordered_num_directives = OrderedDict(
(k, self.num_directives[k])
for k in (resolve_date_order(settings.DATE_ORDER, lst=True))
)
skip_index = []
skip_component = None
for index, token_type in enumerate(self.filtered_tokens):
if index in skip_index:
continue
token, type = token_type
if token in settings.SKIP_TOKENS_PARSER:
continue
if self.time is None:
try:
microsecond = MICROSECOND.search(
self.filtered_tokens[index + 1][0]
).group()
_is_after_time_token = token.index(":")
_is_after_period = self.tokens[self.tokens.index((token, 0)) + 1][
0
].index(".")
except:
microsecond = None
if microsecond:
mindex = index + 2
else:
mindex = index + 1
try:
meridian = MERIDIAN.search(self.filtered_tokens[mindex][0]).group()
except:
meridian = None
if any([":" in token, meridian, microsecond]):
if meridian and not microsecond:
self._token_time = "%s %s" % (token, meridian)
skip_index.append(mindex)
elif microsecond and not meridian:
self._token_time = "%s.%s" % (token, microsecond)
skip_index.append(index + 1)
elif meridian and microsecond:
self._token_time = "%s.%s %s" % (token, microsecond, meridian)
skip_index.append(index + 1)
skip_index.append(mindex)
else:
self._token_time = token
self.time = lambda: time_parser(self._token_time)
continue
results = self._parse(
type, token, settings.FUZZY, skip_component=skip_component
)
for res in results:
if len(token) == 4 and res[0] == "year":
skip_component = "year"
setattr(self, *res)
known, unknown = get_unresolved_attrs(self)
params = {}
for attr in known:
params.update({attr: getattr(self, attr)})
for attr in unknown:
for token, type, _ in self.unset_tokens:
if type == 0:
params.update({attr: int(token)})
datetime(**params)
setattr(self, "_token_%s" % attr, token)
setattr(self, attr, int(token))
|
https://github.com/scrapinghub/dateparser/issues/336
|
Python 3.6.2 (default, Jul 17 2017, 23:14:31)
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
import dateparser
dateparser.__version__
'0.6.0'
dateparser.parse('+38 (0352)')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/conf.py", line 84, in wrapper
return f(*args, **kwargs)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/__init__.py", line 40, in parse
data = parser.get_date_data(date_string, date_formats)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date.py", line 371, in get_date_data
language, date_string, date_formats, settings=self._settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date.py", line 168, in parse
return instance._parse()
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date.py", line 178, in _parse
date_obj = parser()
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date.py", line 199, in _try_parser
self._get_translated_date(), settings=self._settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/conf.py", line 84, in wrapper
return f(*args, **kwargs)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date_parser.py", line 26, in parse
date_obj, period = parse(date_string, settings=settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/parser.py", line 84, in parse
raise exceptions.pop(-1)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/parser.py", line 78, in parse
res = parser(datestring, settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/parser.py", line 454, in parse
po = cls(tokens.tokenize(), settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/parser.py", line 288, in __init__
datetime(**params)
TypeError: Required argument 'day' (pos 3) not found
dateparser.parse('+38 0352')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/conf.py", line 84, in wrapper
return f(*args, **kwargs)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/__init__.py", line 40, in parse
data = parser.get_date_data(date_string, date_formats)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date.py", line 371, in get_date_data
language, date_string, date_formats, settings=self._settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date.py", line 168, in parse
return instance._parse()
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date.py", line 178, in _parse
date_obj = parser()
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date.py", line 199, in _try_parser
self._get_translated_date(), settings=self._settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/conf.py", line 84, in wrapper
return f(*args, **kwargs)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/date_parser.py", line 26, in parse
date_obj, period = parse(date_string, settings=settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/parser.py", line 84, in parse
raise exceptions.pop(-1)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/parser.py", line 78, in parse
res = parser(datestring, settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/parser.py", line 454, in parse
po = cls(tokens.tokenize(), settings)
File "/home/amorgun/env3.6/lib/python3.6/site-packages/dateparser/parser.py", line 288, in __init__
datetime(**params)
TypeError: Required argument 'day' (pos 3) not found
|
TypeError
|
def read_my_cnf_files(self, files, keys):
"""
Reads a list of config files and merges them. The last one will win.
:param files: list of files to read
:param keys: list of keys to retrieve
:returns: tuple, with None for missing keys.
"""
cnf = read_config_files(files)
sections = ["client"]
if self.login_path and self.login_path != "client":
sections.append(self.login_path)
if self.defaults_suffix:
sections.extend([sect + self.defaults_suffix for sect in sections])
def get(key):
result = None
for sect in cnf:
if sect in sections and key in cnf[sect]:
result = cnf[sect][key]
# HACK: if result is a list, then ConfigObj() probably decoded from
# string by splitting on comma, so reconstruct string by joining on
# comma.
if isinstance(result, list):
result = ",".join(result)
return result
return {x: get(x) for x in keys}
|
def read_my_cnf_files(self, files, keys):
"""
Reads a list of config files and merges them. The last one will win.
:param files: list of files to read
:param keys: list of keys to retrieve
:returns: tuple, with None for missing keys.
"""
cnf = read_config_files(files)
sections = ["client"]
if self.login_path and self.login_path != "client":
sections.append(self.login_path)
if self.defaults_suffix:
sections.extend([sect + self.defaults_suffix for sect in sections])
def get(key):
result = None
for sect in cnf:
if sect in sections and key in cnf[sect]:
result = cnf[sect][key]
return result
return {x: get(x) for x in keys}
|
https://github.com/dbcli/mycli/issues/624
|
2018-07-22 01:30:33,368 (48024/MainThread) mycli.main ERROR - traceback: 'Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/mycli/main.py", line 445, in connect
_connect()
File "/usr/local/lib/python3.7/site-packages/mycli/main.py", line 398, in _connect
socket, charset, local_infile, ssl)
File "/usr/local/lib/python3.7/site-packages/mycli/sqlexecute.py", line 52, in __init__
self.connect()
File "/usr/local/lib/python3.7/site-packages/mycli/sqlexecute.py", line 88, in connect
conv=conv, ssl=ssl)
File "/usr/local/lib/python3.7/site-packages/pymysql/__init__.py", line 94, in Connect
return Connection(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pymysql/connections.py", line 327, in __init__
self.connect()
File "/usr/local/lib/python3.7/site-packages/pymysql/connections.py", line 598, in connect
self._request_authentication()
File "/usr/local/lib/python3.7/site-packages/pymysql/connections.py", line 808, in _request_authentication
authresp = _auth.scramble_native_password(self.password, self.salt)
File "/usr/local/lib/python3.7/site-packages/pymysql/_auth.py", line 31, in scramble_native_password
stage1 = sha1_new(password).digest()
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/hashlib.py", line 149, in __hash_new
return _hashlib.new(name, data)
TypeError: object supporting the buffer API required
'
|
TypeError
|
def get(key):
result = None
for sect in cnf:
if sect in sections and key in cnf[sect]:
result = cnf[sect][key]
# HACK: if result is a list, then ConfigObj() probably decoded from
# string by splitting on comma, so reconstruct string by joining on
# comma.
if isinstance(result, list):
result = ",".join(result)
return result
|
def get(key):
result = None
for sect in cnf:
if sect in sections and key in cnf[sect]:
result = cnf[sect][key]
return result
|
https://github.com/dbcli/mycli/issues/624
|
2018-07-22 01:30:33,368 (48024/MainThread) mycli.main ERROR - traceback: 'Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/mycli/main.py", line 445, in connect
_connect()
File "/usr/local/lib/python3.7/site-packages/mycli/main.py", line 398, in _connect
socket, charset, local_infile, ssl)
File "/usr/local/lib/python3.7/site-packages/mycli/sqlexecute.py", line 52, in __init__
self.connect()
File "/usr/local/lib/python3.7/site-packages/mycli/sqlexecute.py", line 88, in connect
conv=conv, ssl=ssl)
File "/usr/local/lib/python3.7/site-packages/pymysql/__init__.py", line 94, in Connect
return Connection(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pymysql/connections.py", line 327, in __init__
self.connect()
File "/usr/local/lib/python3.7/site-packages/pymysql/connections.py", line 598, in connect
self._request_authentication()
File "/usr/local/lib/python3.7/site-packages/pymysql/connections.py", line 808, in _request_authentication
authresp = _auth.scramble_native_password(self.password, self.salt)
File "/usr/local/lib/python3.7/site-packages/pymysql/_auth.py", line 31, in scramble_native_password
stage1 = sha1_new(password).digest()
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/hashlib.py", line 149, in __hash_new
return _hashlib.new(name, data)
TypeError: object supporting the buffer API required
'
|
TypeError
|
def extract_from_part(parsed, stop_at_punctuation=True):
tbl_prefix_seen = False
for item in parsed.tokens:
if tbl_prefix_seen:
if is_subselect(item):
for x in extract_from_part(item, stop_at_punctuation):
yield x
elif stop_at_punctuation and item.ttype is Punctuation:
return
# An incomplete nested select won't be recognized correctly as a
# sub-select. eg: 'SELECT * FROM (SELECT id FROM user'. This causes
# the second FROM to trigger this elif condition resulting in a
# StopIteration. So we need to ignore the keyword if the keyword
# FROM.
# Also 'SELECT * FROM abc JOIN def' will trigger this elif
# condition. So we need to ignore the keyword JOIN and its variants
# INNER JOIN, FULL OUTER JOIN, etc.
elif (
item.ttype is Keyword
and (not item.value.upper() == "FROM")
and (not item.value.upper().endswith("JOIN"))
):
return
else:
yield item
elif (
item.ttype is Keyword or item.ttype is Keyword.DML
) and item.value.upper() in (
"COPY",
"FROM",
"INTO",
"UPDATE",
"TABLE",
"JOIN",
):
tbl_prefix_seen = True
# 'SELECT a, FROM abc' will detect FROM as part of the column list.
# So this check here is necessary.
elif isinstance(item, IdentifierList):
for identifier in item.get_identifiers():
if identifier.ttype is Keyword and identifier.value.upper() == "FROM":
tbl_prefix_seen = True
break
|
def extract_from_part(parsed, stop_at_punctuation=True):
tbl_prefix_seen = False
for item in parsed.tokens:
if tbl_prefix_seen:
if is_subselect(item):
for x in extract_from_part(item, stop_at_punctuation):
yield x
elif stop_at_punctuation and item.ttype is Punctuation:
raise StopIteration
# An incomplete nested select won't be recognized correctly as a
# sub-select. eg: 'SELECT * FROM (SELECT id FROM user'. This causes
# the second FROM to trigger this elif condition resulting in a
# StopIteration. So we need to ignore the keyword if the keyword
# FROM.
# Also 'SELECT * FROM abc JOIN def' will trigger this elif
# condition. So we need to ignore the keyword JOIN and its variants
# INNER JOIN, FULL OUTER JOIN, etc.
elif (
item.ttype is Keyword
and (not item.value.upper() == "FROM")
and (not item.value.upper().endswith("JOIN"))
):
raise StopIteration
else:
yield item
elif (
item.ttype is Keyword or item.ttype is Keyword.DML
) and item.value.upper() in (
"COPY",
"FROM",
"INTO",
"UPDATE",
"TABLE",
"JOIN",
):
tbl_prefix_seen = True
# 'SELECT a, FROM abc' will detect FROM as part of the column list.
# So this check here is necessary.
elif isinstance(item, IdentifierList):
for identifier in item.get_identifiers():
if identifier.ttype is Keyword and identifier.value.upper() == "FROM":
tbl_prefix_seen = True
break
|
https://github.com/dbcli/mycli/issues/619
|
Traceback (most recent call last):
File "c:\python37\lib\site-packages\mycli\packages\parseutils.py", line 95, in extract_from_part
raise StopIteration
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):w to complete suggestion
File "c:\python37\lib\threading.py", line 917, in _bootstrap_inner
self.run()
File "c:\python37\lib\threading.py", line 865, in run
self._target(*self._args, **self._kwargs)
File "c:\python37\lib\site-packages\prompt_toolkit\interface.py", line 865, in run
completions = list(buffer.completer.get_completions(document, complete_event))
File "c:\python37\lib\site-packages\mycli\sqlcompleter.py", line 258, in get_completions
suggestions = suggest_type(document.text, document.text_before_cursor)
File "c:\python37\lib\site-packages\mycli\packages\completion_engine.py", line 93, in suggest_type
full_text, identifier)
File "c:\python37\lib\site-packages\mycli\packages\completion_engine.py", line 203, in suggest_based_on_last_token
return [{'type': 'column', 'tables': extract_tables(full_text)}]
File "c:\python37\lib\site-packages\mycli\packages\parseutils.py", line 154, in extract_tables
return list(extract_table_identifiers(stream))
File "c:\python37\lib\site-packages\mycli\packages\parseutils.py", line 113, in extract_table_identifiers
for item in token_stream:
RuntimeError: generator raised StopIteration
|
RuntimeError
|
def watch_query(arg, **kwargs):
usage = """Syntax: watch [seconds] [-c] query.
* seconds: The interval at the query will be repeated, in seconds.
By default 5.
* -c: Clears the screen between every iteration.
"""
if not arg:
yield (None, None, None, usage)
return
seconds = 5
clear_screen = False
statement = None
while statement is None:
arg = arg.strip()
if not arg:
# Oops, we parsed all the arguments without finding a statement
yield (None, None, None, usage)
return
(current_arg, _, arg) = arg.partition(" ")
try:
seconds = float(current_arg)
continue
except ValueError:
pass
if current_arg == "-c":
clear_screen = True
continue
statement = "{0!s} {1!s}".format(current_arg, arg)
destructive_prompt = confirm_destructive_query(statement)
if destructive_prompt is False:
click.secho("Wise choice!")
return
elif destructive_prompt is True:
click.secho("Your call!")
cur = kwargs["cur"]
sql_list = [
(sql.rstrip(";"), "> {0!s}".format(sql)) for sql in sqlparse.split(statement)
]
old_pager_enabled = is_pager_enabled()
while True:
if clear_screen:
click.clear()
try:
# Somewhere in the code the pager its activated after every yield,
# so we disable it in every iteration
set_pager_enabled(False)
for sql, title in sql_list:
cur.execute(sql)
if cur.description:
headers = [x[0] for x in cur.description]
yield (title, cur, headers, None)
else:
yield (title, None, None, None)
sleep(seconds)
except KeyboardInterrupt:
# This prints the Ctrl-C character in its own line, which prevents
# to print a line with the cursor positioned behind the prompt
click.secho("", nl=True)
return
finally:
set_pager_enabled(old_pager_enabled)
|
def watch_query(arg, **kwargs):
usage = """Syntax: watch [seconds] [-c] query.
* seconds: The interval at the query will be repeated, in seconds.
By default 5.
* -c: Clears the screen between every iteration.
"""
if not arg:
yield (None, None, None, usage)
raise StopIteration
seconds = 5
clear_screen = False
statement = None
while statement is None:
arg = arg.strip()
if not arg:
# Oops, we parsed all the arguments without finding a statement
yield (None, None, None, usage)
raise StopIteration
(current_arg, _, arg) = arg.partition(" ")
try:
seconds = float(current_arg)
continue
except ValueError:
pass
if current_arg == "-c":
clear_screen = True
continue
statement = "{0!s} {1!s}".format(current_arg, arg)
destructive_prompt = confirm_destructive_query(statement)
if destructive_prompt is False:
click.secho("Wise choice!")
raise StopIteration
elif destructive_prompt is True:
click.secho("Your call!")
cur = kwargs["cur"]
sql_list = [
(sql.rstrip(";"), "> {0!s}".format(sql)) for sql in sqlparse.split(statement)
]
old_pager_enabled = is_pager_enabled()
while True:
if clear_screen:
click.clear()
try:
# Somewhere in the code the pager its activated after every yield,
# so we disable it in every iteration
set_pager_enabled(False)
for sql, title in sql_list:
cur.execute(sql)
if cur.description:
headers = [x[0] for x in cur.description]
yield (title, cur, headers, None)
else:
yield (title, None, None, None)
sleep(seconds)
except KeyboardInterrupt:
# This prints the Ctrl-C character in its own line, which prevents
# to print a line with the cursor positioned behind the prompt
click.secho("", nl=True)
raise StopIteration
finally:
set_pager_enabled(old_pager_enabled)
|
https://github.com/dbcli/mycli/issues/619
|
Traceback (most recent call last):
File "c:\python37\lib\site-packages\mycli\packages\parseutils.py", line 95, in extract_from_part
raise StopIteration
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):w to complete suggestion
File "c:\python37\lib\threading.py", line 917, in _bootstrap_inner
self.run()
File "c:\python37\lib\threading.py", line 865, in run
self._target(*self._args, **self._kwargs)
File "c:\python37\lib\site-packages\prompt_toolkit\interface.py", line 865, in run
completions = list(buffer.completer.get_completions(document, complete_event))
File "c:\python37\lib\site-packages\mycli\sqlcompleter.py", line 258, in get_completions
suggestions = suggest_type(document.text, document.text_before_cursor)
File "c:\python37\lib\site-packages\mycli\packages\completion_engine.py", line 93, in suggest_type
full_text, identifier)
File "c:\python37\lib\site-packages\mycli\packages\completion_engine.py", line 203, in suggest_based_on_last_token
return [{'type': 'column', 'tables': extract_tables(full_text)}]
File "c:\python37\lib\site-packages\mycli\packages\parseutils.py", line 154, in extract_tables
return list(extract_table_identifiers(stream))
File "c:\python37\lib\site-packages\mycli\packages\parseutils.py", line 113, in extract_table_identifiers
for item in token_stream:
RuntimeError: generator raised StopIteration
|
RuntimeError
|
def initialize_logging(self):
log_file = os.path.expanduser(self.config["main"]["log_file"])
log_level = self.config["main"]["log_level"]
level_map = {
"CRITICAL": logging.CRITICAL,
"ERROR": logging.ERROR,
"WARNING": logging.WARNING,
"INFO": logging.INFO,
"DEBUG": logging.DEBUG,
}
# Disable logging if value is NONE by switching to a no-op handler
# Set log level to a high value so it doesn't even waste cycles getting called.
if log_level.upper() == "NONE":
handler = logging.NullHandler()
log_level = "CRITICAL"
elif dir_path_exists(log_file):
handler = logging.FileHandler(log_file)
else:
self.echo(
'Error: Unable to open the log file "{}".'.format(log_file),
err=True,
fg="red",
)
return
formatter = logging.Formatter(
"%(asctime)s (%(process)d/%(threadName)s) %(name)s %(levelname)s - %(message)s"
)
handler.setFormatter(formatter)
root_logger = logging.getLogger("mycli")
root_logger.addHandler(handler)
root_logger.setLevel(level_map[log_level.upper()])
logging.captureWarnings(True)
root_logger.debug("Initializing mycli logging.")
root_logger.debug("Log file %r.", log_file)
|
def initialize_logging(self):
log_file = self.config["main"]["log_file"]
log_level = self.config["main"]["log_level"]
level_map = {
"CRITICAL": logging.CRITICAL,
"ERROR": logging.ERROR,
"WARNING": logging.WARNING,
"INFO": logging.INFO,
"DEBUG": logging.DEBUG,
}
# Disable logging if value is NONE by switching to a no-op handler
# Set log level to a high value so it doesn't even waste cycles getting called.
if log_level.upper() == "NONE":
handler = logging.NullHandler()
log_level = "CRITICAL"
else:
handler = logging.FileHandler(os.path.expanduser(log_file))
formatter = logging.Formatter(
"%(asctime)s (%(process)d/%(threadName)s) %(name)s %(levelname)s - %(message)s"
)
handler.setFormatter(formatter)
root_logger = logging.getLogger("mycli")
root_logger.addHandler(handler)
root_logger.setLevel(level_map[log_level.upper()])
logging.captureWarnings(True)
root_logger.debug("Initializing mycli logging.")
root_logger.debug("Log file %r.", log_file)
|
https://github.com/dbcli/mycli/issues/569
|
$ mycli
Password:
localhost:(none)> use test
Traceback (most recent call last):
File "/home/linuxbrew/.linuxbrew/bin/mycli", line 11, in <module>
load_entry_point('mycli==1.16.0', 'console_scripts', 'mycli')()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/mycli/main.py", line 1053, in cli
mycli.run_cli()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/mycli/main.py", line 696, in run_cli
one_iteration()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/mycli/main.py", line 512, in one_iteration
document = self.cli.run()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/interface.py", line 415, in run
self.eventloop.run(self.input, self.create_eventloop_callbacks())
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/eventloop/posix.py", line 159, in run
t()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/eventloop/posix.py", line 82, in read_from_stdin
inputstream.feed(data)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/terminal/vt100_input.py", line 398, in feed
self._input_parser.send(c)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/terminal/vt100_input.py", line 307, in _input_parser_generator
self._call_handler(match, prefix)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/terminal/vt100_input.py", line 340, in _call_handler
self.feed_key_callback(KeyPress(key, insert_text))
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/interface.py", line 1048, in feed_key
cli.input_processor.process_keys()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/input_processor.py", line 219, in process_keys
self._process_coroutine.send(key_press)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/input_processor.py", line 176, in _process
self._call_handler(matches[-1], key_sequence=buffer[:])
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/input_processor.py", line 247, in _call_handler
handler.call(event)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/registry.py", line 61, in call
return self.handler(event)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/bindings/basic.py", line 167, in _
buff.accept_action.validate_and_handle(event.cli, buff)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/buffer.py", line 86, in validate_and_handle
buffer.append_to_history()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/buffer.py", line 1130, in append_to_history
self.history.append(self.text)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/history.py", line 105, in append
with open(self.filename, 'ab') as f:
IOError: [Errno 2] No such file or directory: '/home/tsr/.cache/mycli/history'
|
IOError
|
def run_cli(self):
iterations = 0
sqlexecute = self.sqlexecute
logger = self.logger
self.configure_pager()
if self.smart_completion:
self.refresh_completions()
author_file = os.path.join(PACKAGE_ROOT, "AUTHORS")
sponsor_file = os.path.join(PACKAGE_ROOT, "SPONSORS")
history_file = os.path.expanduser(
os.environ.get("MYCLI_HISTFILE", "~/.mycli-history")
)
if dir_path_exists(history_file):
history = FileHistory(history_file)
else:
history = None
self.echo(
'Error: Unable to open the history file "{}". '
"Your query history will not be saved.".format(history_file),
err=True,
fg="red",
)
key_binding_manager = mycli_bindings()
if not self.less_chatty:
print("Version:", __version__)
print("Chat: https://gitter.im/dbcli/mycli")
print("Mail: https://groups.google.com/forum/#!forum/mycli-users")
print("Home: http://mycli.net")
print("Thanks to the contributor -", thanks_picker([author_file, sponsor_file]))
def prompt_tokens(cli):
prompt = self.get_prompt(self.prompt_format)
if (
self.prompt_format == self.default_prompt
and len(prompt) > self.max_len_prompt
):
prompt = self.get_prompt("\\d> ")
return [(Token.Prompt, prompt)]
def get_continuation_tokens(cli, width):
continuation_prompt = self.get_prompt(self.prompt_continuation_format)
return [
(
Token.Continuation,
" " * (width - len(continuation_prompt)) + continuation_prompt,
)
]
def show_suggestion_tip():
return iterations < 2
def one_iteration(document=None):
if document is None:
document = self.cli.run()
special.set_expanded_output(False)
try:
document = self.handle_editor_command(self.cli, document)
except RuntimeError as e:
logger.error("sql: %r, error: %r", document.text, e)
logger.error("traceback: %r", traceback.format_exc())
self.echo(str(e), err=True, fg="red")
return
if not document.text.strip():
return
if self.destructive_warning:
destroy = confirm_destructive_query(document.text)
if destroy is None:
pass # Query was not destructive. Nothing to do here.
elif destroy is True:
self.echo("Your call!")
else:
self.echo("Wise choice!")
return
# Keep track of whether or not the query is mutating. In case
# of a multi-statement query, the overall query is considered
# mutating if any one of the component statements is mutating
mutating = False
try:
logger.debug("sql: %r", document.text)
special.write_tee(self.get_prompt(self.prompt_format) + document.text)
if self.logfile:
self.logfile.write("\n# %s\n" % datetime.now())
self.logfile.write(document.text)
self.logfile.write("\n")
successful = False
start = time()
res = sqlexecute.run(document.text)
self.formatter.query = document.text
successful = True
result_count = 0
for title, cur, headers, status in res:
logger.debug("headers: %r", headers)
logger.debug("rows: %r", cur)
logger.debug("status: %r", status)
threshold = 1000
if is_select(status) and cur and cur.rowcount > threshold:
self.echo(
"The result set has more than {} rows.".format(threshold),
fg="red",
)
if not click.confirm("Do you want to continue?"):
self.echo("Aborted!", err=True, fg="red")
break
if self.auto_vertical_output:
max_width = self.cli.output.get_size().columns
else:
max_width = None
formatted = self.format_output(
title, cur, headers, special.is_expanded_output(), max_width
)
t = time() - start
try:
if result_count > 0:
self.echo("")
try:
self.output(formatted, status)
except KeyboardInterrupt:
pass
if special.is_timing_enabled():
self.echo("Time: %0.03fs" % t)
except KeyboardInterrupt:
pass
start = time()
result_count += 1
mutating = mutating or is_mutating(status)
special.unset_once_if_written()
except EOFError as e:
raise e
except KeyboardInterrupt:
# get last connection id
connection_id_to_kill = sqlexecute.connection_id
logger.debug("connection id to kill: %r", connection_id_to_kill)
# Restart connection to the database
sqlexecute.connect()
try:
for title, cur, headers, status in sqlexecute.run(
"kill %s" % connection_id_to_kill
):
status_str = str(status).lower()
if status_str.find("ok") > -1:
logger.debug(
"cancelled query, connection id: %r, sql: %r",
connection_id_to_kill,
document.text,
)
self.echo("cancelled query", err=True, fg="red")
except Exception as e:
self.echo(
"Encountered error while cancelling query: {}".format(e),
err=True,
fg="red",
)
except NotImplementedError:
self.echo("Not Yet Implemented.", fg="yellow")
except OperationalError as e:
logger.debug("Exception: %r", e)
if e.args[0] in (2003, 2006, 2013):
logger.debug("Attempting to reconnect.")
self.echo("Reconnecting...", fg="yellow")
try:
sqlexecute.connect()
logger.debug("Reconnected successfully.")
one_iteration(document)
return # OK to just return, cuz the recursion call runs to the end.
except OperationalError as e:
logger.debug("Reconnect failed. e: %r", e)
self.echo(str(e), err=True, fg="red")
# If reconnection failed, don't proceed further.
return
else:
logger.error("sql: %r, error: %r", document.text, e)
logger.error("traceback: %r", traceback.format_exc())
self.echo(str(e), err=True, fg="red")
except Exception as e:
logger.error("sql: %r, error: %r", document.text, e)
logger.error("traceback: %r", traceback.format_exc())
self.echo(str(e), err=True, fg="red")
else:
if is_dropping_database(document.text, self.sqlexecute.dbname):
self.sqlexecute.dbname = None
self.sqlexecute.connect()
# Refresh the table names and column names if necessary.
if need_completion_refresh(document.text):
self.refresh_completions(reset=need_completion_reset(document.text))
finally:
if self.logfile is False:
self.echo("Warning: This query was not logged.", err=True, fg="red")
query = Query(document.text, successful, mutating)
self.query_history.append(query)
get_toolbar_tokens = create_toolbar_tokens_func(
self.completion_refresher.is_refreshing, show_suggestion_tip
)
layout = create_prompt_layout(
lexer=MyCliLexer,
multiline=True,
get_prompt_tokens=prompt_tokens,
get_continuation_tokens=get_continuation_tokens,
get_bottom_toolbar_tokens=get_toolbar_tokens,
display_completions_in_columns=self.wider_completion_menu,
extra_input_processors=[
ConditionalProcessor(
processor=HighlightMatchingBracketProcessor(chars="[](){}"),
filter=HasFocus(DEFAULT_BUFFER) & ~IsDone(),
)
],
reserve_space_for_menu=self.get_reserved_space(),
)
with self._completer_lock:
buf = CLIBuffer(
always_multiline=self.multi_line,
completer=self.completer,
history=history,
auto_suggest=AutoSuggestFromHistory(),
complete_while_typing=Always(),
accept_action=AcceptAction.RETURN_DOCUMENT,
)
if self.key_bindings == "vi":
editing_mode = EditingMode.VI
else:
editing_mode = EditingMode.EMACS
application = Application(
style=style_from_pygments(style_cls=self.output_style),
layout=layout,
buffer=buf,
key_bindings_registry=key_binding_manager.registry,
on_exit=AbortAction.RAISE_EXCEPTION,
on_abort=AbortAction.RETRY,
editing_mode=editing_mode,
ignore_case=True,
)
self.cli = CommandLineInterface(
application=application, eventloop=create_eventloop()
)
try:
while True:
one_iteration()
iterations += 1
except EOFError:
special.close_tee()
if not self.less_chatty:
self.echo("Goodbye!")
|
def run_cli(self):
iterations = 0
sqlexecute = self.sqlexecute
logger = self.logger
self.configure_pager()
if self.smart_completion:
self.refresh_completions()
author_file = os.path.join(PACKAGE_ROOT, "AUTHORS")
sponsor_file = os.path.join(PACKAGE_ROOT, "SPONSORS")
key_binding_manager = mycli_bindings()
if not self.less_chatty:
print("Version:", __version__)
print("Chat: https://gitter.im/dbcli/mycli")
print("Mail: https://groups.google.com/forum/#!forum/mycli-users")
print("Home: http://mycli.net")
print("Thanks to the contributor -", thanks_picker([author_file, sponsor_file]))
def prompt_tokens(cli):
prompt = self.get_prompt(self.prompt_format)
if (
self.prompt_format == self.default_prompt
and len(prompt) > self.max_len_prompt
):
prompt = self.get_prompt("\\d> ")
return [(Token.Prompt, prompt)]
def get_continuation_tokens(cli, width):
continuation_prompt = self.get_prompt(self.prompt_continuation_format)
return [
(
Token.Continuation,
" " * (width - len(continuation_prompt)) + continuation_prompt,
)
]
def show_suggestion_tip():
return iterations < 2
def one_iteration(document=None):
if document is None:
document = self.cli.run()
special.set_expanded_output(False)
try:
document = self.handle_editor_command(self.cli, document)
except RuntimeError as e:
logger.error("sql: %r, error: %r", document.text, e)
logger.error("traceback: %r", traceback.format_exc())
self.echo(str(e), err=True, fg="red")
return
if not document.text.strip():
return
if self.destructive_warning:
destroy = confirm_destructive_query(document.text)
if destroy is None:
pass # Query was not destructive. Nothing to do here.
elif destroy is True:
self.echo("Your call!")
else:
self.echo("Wise choice!")
return
# Keep track of whether or not the query is mutating. In case
# of a multi-statement query, the overall query is considered
# mutating if any one of the component statements is mutating
mutating = False
try:
logger.debug("sql: %r", document.text)
special.write_tee(self.get_prompt(self.prompt_format) + document.text)
if self.logfile:
self.logfile.write("\n# %s\n" % datetime.now())
self.logfile.write(document.text)
self.logfile.write("\n")
successful = False
start = time()
res = sqlexecute.run(document.text)
self.formatter.query = document.text
successful = True
result_count = 0
for title, cur, headers, status in res:
logger.debug("headers: %r", headers)
logger.debug("rows: %r", cur)
logger.debug("status: %r", status)
threshold = 1000
if is_select(status) and cur and cur.rowcount > threshold:
self.echo(
"The result set has more than {} rows.".format(threshold),
fg="red",
)
if not click.confirm("Do you want to continue?"):
self.echo("Aborted!", err=True, fg="red")
break
if self.auto_vertical_output:
max_width = self.cli.output.get_size().columns
else:
max_width = None
formatted = self.format_output(
title, cur, headers, special.is_expanded_output(), max_width
)
t = time() - start
try:
if result_count > 0:
self.echo("")
try:
self.output(formatted, status)
except KeyboardInterrupt:
pass
if special.is_timing_enabled():
self.echo("Time: %0.03fs" % t)
except KeyboardInterrupt:
pass
start = time()
result_count += 1
mutating = mutating or is_mutating(status)
special.unset_once_if_written()
except EOFError as e:
raise e
except KeyboardInterrupt:
# get last connection id
connection_id_to_kill = sqlexecute.connection_id
logger.debug("connection id to kill: %r", connection_id_to_kill)
# Restart connection to the database
sqlexecute.connect()
try:
for title, cur, headers, status in sqlexecute.run(
"kill %s" % connection_id_to_kill
):
status_str = str(status).lower()
if status_str.find("ok") > -1:
logger.debug(
"cancelled query, connection id: %r, sql: %r",
connection_id_to_kill,
document.text,
)
self.echo("cancelled query", err=True, fg="red")
except Exception as e:
self.echo(
"Encountered error while cancelling query: {}".format(e),
err=True,
fg="red",
)
except NotImplementedError:
self.echo("Not Yet Implemented.", fg="yellow")
except OperationalError as e:
logger.debug("Exception: %r", e)
if e.args[0] in (2003, 2006, 2013):
logger.debug("Attempting to reconnect.")
self.echo("Reconnecting...", fg="yellow")
try:
sqlexecute.connect()
logger.debug("Reconnected successfully.")
one_iteration(document)
return # OK to just return, cuz the recursion call runs to the end.
except OperationalError as e:
logger.debug("Reconnect failed. e: %r", e)
self.echo(str(e), err=True, fg="red")
# If reconnection failed, don't proceed further.
return
else:
logger.error("sql: %r, error: %r", document.text, e)
logger.error("traceback: %r", traceback.format_exc())
self.echo(str(e), err=True, fg="red")
except Exception as e:
logger.error("sql: %r, error: %r", document.text, e)
logger.error("traceback: %r", traceback.format_exc())
self.echo(str(e), err=True, fg="red")
else:
if is_dropping_database(document.text, self.sqlexecute.dbname):
self.sqlexecute.dbname = None
self.sqlexecute.connect()
# Refresh the table names and column names if necessary.
if need_completion_refresh(document.text):
self.refresh_completions(reset=need_completion_reset(document.text))
finally:
if self.logfile is False:
self.echo("Warning: This query was not logged.", err=True, fg="red")
query = Query(document.text, successful, mutating)
self.query_history.append(query)
get_toolbar_tokens = create_toolbar_tokens_func(
self.completion_refresher.is_refreshing, show_suggestion_tip
)
layout = create_prompt_layout(
lexer=MyCliLexer,
multiline=True,
get_prompt_tokens=prompt_tokens,
get_continuation_tokens=get_continuation_tokens,
get_bottom_toolbar_tokens=get_toolbar_tokens,
display_completions_in_columns=self.wider_completion_menu,
extra_input_processors=[
ConditionalProcessor(
processor=HighlightMatchingBracketProcessor(chars="[](){}"),
filter=HasFocus(DEFAULT_BUFFER) & ~IsDone(),
)
],
reserve_space_for_menu=self.get_reserved_space(),
)
with self._completer_lock:
buf = CLIBuffer(
always_multiline=self.multi_line,
completer=self.completer,
history=FileHistory(
os.path.expanduser(os.environ.get("MYCLI_HISTFILE", "~/.mycli-history"))
),
auto_suggest=AutoSuggestFromHistory(),
complete_while_typing=Always(),
accept_action=AcceptAction.RETURN_DOCUMENT,
)
if self.key_bindings == "vi":
editing_mode = EditingMode.VI
else:
editing_mode = EditingMode.EMACS
application = Application(
style=style_from_pygments(style_cls=self.output_style),
layout=layout,
buffer=buf,
key_bindings_registry=key_binding_manager.registry,
on_exit=AbortAction.RAISE_EXCEPTION,
on_abort=AbortAction.RETRY,
editing_mode=editing_mode,
ignore_case=True,
)
self.cli = CommandLineInterface(
application=application, eventloop=create_eventloop()
)
try:
while True:
one_iteration()
iterations += 1
except EOFError:
special.close_tee()
if not self.less_chatty:
self.echo("Goodbye!")
|
https://github.com/dbcli/mycli/issues/569
|
$ mycli
Password:
localhost:(none)> use test
Traceback (most recent call last):
File "/home/linuxbrew/.linuxbrew/bin/mycli", line 11, in <module>
load_entry_point('mycli==1.16.0', 'console_scripts', 'mycli')()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/mycli/main.py", line 1053, in cli
mycli.run_cli()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/mycli/main.py", line 696, in run_cli
one_iteration()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/mycli/main.py", line 512, in one_iteration
document = self.cli.run()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/interface.py", line 415, in run
self.eventloop.run(self.input, self.create_eventloop_callbacks())
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/eventloop/posix.py", line 159, in run
t()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/eventloop/posix.py", line 82, in read_from_stdin
inputstream.feed(data)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/terminal/vt100_input.py", line 398, in feed
self._input_parser.send(c)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/terminal/vt100_input.py", line 307, in _input_parser_generator
self._call_handler(match, prefix)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/terminal/vt100_input.py", line 340, in _call_handler
self.feed_key_callback(KeyPress(key, insert_text))
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/interface.py", line 1048, in feed_key
cli.input_processor.process_keys()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/input_processor.py", line 219, in process_keys
self._process_coroutine.send(key_press)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/input_processor.py", line 176, in _process
self._call_handler(matches[-1], key_sequence=buffer[:])
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/input_processor.py", line 247, in _call_handler
handler.call(event)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/registry.py", line 61, in call
return self.handler(event)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/key_binding/bindings/basic.py", line 167, in _
buff.accept_action.validate_and_handle(event.cli, buff)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/buffer.py", line 86, in validate_and_handle
buffer.append_to_history()
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/buffer.py", line 1130, in append_to_history
self.history.append(self.text)
File "/home/linuxbrew/.linuxbrew/Cellar/mycli/1.16.0/libexec/lib/python2.7/site-packages/prompt_toolkit/history.py", line 105, in append
with open(self.filename, 'ab') as f:
IOError: [Errno 2] No such file or directory: '/home/tsr/.cache/mycli/history'
|
IOError
|
def _mount_references(self):
"""
Find the references that is defined in self.configuration
:return:
"""
self.resources_raw = deepcopy(self.resources)
invalid_references = ("var.", "each.")
# This section will link resources found in configuration part of the plan output.
# The reference should be on both ways (A->B, B->A) since terraform sometimes report these references
# in opposite ways, depending on the provider structure.
for resource in self.configuration["resources"]:
if "expressions" in self.configuration["resources"][resource]:
ref_list = {}
for key, value in self.configuration["resources"][resource][
"expressions"
].items():
references = (
seek_key_in_dict(value, "references")
if isinstance(value, (dict, list))
else []
)
valid_references = []
for ref in references:
if isinstance(ref, dict) and ref.get("references"):
valid_references = [
r
for r in ref["references"]
if not r.startswith(invalid_references)
]
for ref in valid_references:
if key not in ref_list:
ref_list[key] = self._find_resource_from_name(ref)
else:
ref_list[key].extend(self._find_resource_from_name(ref))
# This is where we synchronise constant_value in the configuration section with the resource
# for filling up the missing elements that hasn't been defined in the resource due to provider
# implementation.
target_resource = [
t
for t in [self.resources.get(resource, {}).get("address")]
if t is not None
]
if not target_resource:
target_resource = [
k for k in self.resources.keys() if k.startswith(resource)
]
for t_r in target_resource:
if (
type(value) is type(self.resources[t_r]["values"].get(key))
and self.resources[t_r]["values"].get(key) != value
):
if isinstance(value, (list, dict)):
merge_dicts(self.resources[t_r]["values"][key], value)
if ref_list:
ref_type = self.configuration["resources"][resource]["expressions"].get(
"type", {}
)
if "references" in ref_type:
ref_type = resource.split(".")[0]
if not ref_type and not self.is_type(resource, "data"):
resource_type, resource_id = resource.split(".")
ref_type = resource_type
for k, v in ref_list.items():
v = flatten_list(v)
# Mounting A->B
source_resources = self._find_resource_from_name(
self.configuration["resources"][resource]["address"]
)
self._mount_resources(
source=source_resources, target=ref_list, ref_type=ref_type
)
# Mounting B->A
for parameter, target_resources in ref_list.items():
for target_resource in target_resources:
if (
not self.is_type(resource, "data")
and not self.is_type(resource, "var")
and not self.is_type(resource, "provider")
):
ref_type = target_resource.split(".", maxsplit=1)[0]
self._mount_resources(
source=[target_resource],
target={parameter: source_resources},
ref_type=ref_type,
)
|
def _mount_references(self):
"""
Find the references that is defined in self.configuration
:return:
"""
self.resources_raw = deepcopy(self.resources)
invalid_references = ("var.", "each.")
# This section will link resources found in configuration part of the plan output.
# The reference should be on both ways (A->B, B->A) since terraform sometimes report these references
# in opposite ways, depending on the provider structure.
for resource in self.configuration["resources"]:
if "expressions" in self.configuration["resources"][resource]:
ref_list = {}
for key, value in self.configuration["resources"][resource][
"expressions"
].items():
references = (
seek_key_in_dict(value, "references")
if isinstance(value, (dict, list))
else []
)
valid_references = []
for ref in references:
if isinstance(ref, dict) and ref.get("references"):
valid_references = [
r
for r in ref["references"]
if not r.startswith(invalid_references)
]
for ref in valid_references:
if key not in ref_list:
ref_list[key] = self._find_resource_from_name(ref)
else:
ref_list[key].extend(self._find_resource_from_name(ref))
# This is where we synchronise constant_value in the configuration section with the resource
# for filling up the missing elements that hasn't been defined in the resource due to provider
# implementation.
target_resource = [
t
for t in [self.resources.get(resource, {}).get("address")]
if t is not None
]
if not target_resource:
target_resource = [
k for k in self.resources.keys() if k.startswith(resource)
]
if not target_resource:
target_resource = [
k for k in self.resources.keys() if k.endswith(resource)
]
for t_r in target_resource:
if (
type(value) is type(self.resources[t_r]["values"].get(key))
and self.resources[t_r]["values"].get(key) != value
):
if isinstance(value, (list, dict)):
merge_dicts(self.resources[t_r]["values"][key], value)
if ref_list:
ref_type = self.configuration["resources"][resource]["expressions"].get(
"type", {}
)
if not ref_type and not self.is_type(resource, "data"):
resource_type, resource_id = resource.split(".")
ref_type = resource_type
for k, v in ref_list.items():
v = flatten_list(v)
# Mounting A->B
source_resources = self._find_resource_from_name(
self.configuration["resources"][resource]["address"]
)
self._mount_resources(
source=source_resources, target=ref_list, ref_type=ref_type
)
# Mounting B->A
for parameter, target_resources in ref_list.items():
for target_resource in target_resources:
if (
not self.is_type(resource, "data")
and not self.is_type(resource, "var")
and not self.is_type(resource, "provider")
):
ref_type = target_resource.split(".", maxsplit=1)[0]
self._mount_resources(
source=[target_resource],
target={parameter: source_resources},
ref_type=ref_type,
)
|
https://github.com/terraform-compliance/cli/issues/427
|
❗ ERROR: Hook 'load_terraform_data' from /usr/local/lib/python3.7/site-packages/terraform_compliance/steps/terrain.py:8 raised: 'TypeError: unhashable type: 'dict''
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/radish/hookregistry.py", line 132, in call
func(model, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/steps/terrain.py", line 10, in load_terraform_data
world.config.terraform = TerraformParser(world.config.user_data['plan_file'])
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/extensions/terraform.py", line 44, in __init__
self.parse()
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/extensions/terraform.py", line 403, in parse
self._mount_references()
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/extensions/terraform.py", line 359, in _mount_references
ref_type=ref_type)
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/extensions/terraform.py", line 257, in _mount_resources
if ref_type not in self.resources[target_resource]['values']:
TypeError: unhashable type: 'dict'
|
TypeError
|
def _mount_resources(self, source, target, ref_type):
"""
Mounts values of the source resource to the target resource's values with ref_type key
:param source: source resource
:param target: target resource
:param ref_type: reference type (e.g. ingress )
:return: none
"""
for source_resource in source:
if "values" not in self.resources[source_resource]:
continue
for target_resource in target:
if "values" not in self.resources[target_resource]:
continue
if ref_type not in self.resources[target_resource]["values"]:
self.resources[target_resource]["values"][ref_type] = list()
self.resources[target_resource]["values"][ref_type].append(
self.resources[source_resource]["values"]
)
else:
self.resources[target_resource]["values"][ref_type].append(
self.resources[source_resource]["values"]
)
|
def _mount_resources(self, source, target, ref_type):
"""
Mounts values of the source resource to the target resource's values with ref_type key
:param source: source resource
:param target: target resource
:param ref_type: reference type (e.g. ingress )
:return: none
"""
for source_resource in source:
for target_resource in target:
if ref_type not in self.resources[target_resource]["values"]:
self.resources[target_resource]["values"][ref_type] = list()
self.resources[target_resource]["values"][ref_type].append(
self.resources[source_resource]["values"]
)
else:
self.resources[target_resource]["values"][ref_type].append(
self.resources[source_resource]["values"]
)
|
https://github.com/terraform-compliance/cli/issues/124
|
$ terraform-compliance -p /target/tc-test2/tf-template/jenkins.plan.out.json -f /target/tc-test2/features
terraform-compliance v1.0.13 initiated
* Features : /target/tc-test2/features
* Plan File : /target/tc-test2/tf-template/jenkins.plan.out.json
. Running tests.
Feature: Resources should be properly tagged # /target/tc-test2/features/tags.feature
In order to keep track of resource ownership
As engineers
We'll enforce tagging on all resources
2 features (0 passed)
30 scenarios (0 passed)
109 steps (0 passed)
Run 1562934682 finished within a moment
Error: Hook 'load_terraform_data' from /usr/local/lib/python3.7/site-packages/terraform_compliance/steps/terrain.py:5 raised: 'KeyError: 'values''
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/radish/hookregistry.py", line 132, in call
func(model, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/steps/terrain.py", line 7, in load_terraform_data
world.config.terraform = TerraformParser(world.config.user_data['plan_file'])
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/extensions/terraform.py", line 34, in __init__
self.parse()
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/extensions/terraform.py", line 225, in parse
self._mount_references()
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/extensions/terraform.py", line 200, in _mount_references
self._mount_resources(source_resources, flatten_list(ref_list), ref_type)
File "/usr/local/lib/python3.7/site-packages/terraform_compliance/extensions/terraform.py", line 153, in _mount_resources
self.resources[target_resource]['values'][ref_type].append(self.resources[source_resource]['values'])
KeyError: 'values'
|
KeyError
|
def change_value_in_dict(target_dictionary, path_to_change, value_to_change):
if type(path_to_change) is str:
path_to_change = path_to_change.split(".")
if type(path_to_change) is not list:
return False
for x in xrange(0, len(path_to_change)):
for condition in hcl_conditions:
if condition in path_to_change[x]:
return False
path_to_adjust = '["{}"]'.format('"]["'.join(path_to_change))
try:
target = eval("target_dictionary{}".format(path_to_adjust))
for key, value in value_to_change.items():
if "type" in value:
type_key = value["type"]
source = value
source["referenced_name"] = key
if type_key not in target:
target[type_key] = list()
elif type_key in target and type(target[type_key]) is not list:
target[type_key] = [target[type_key]]
target[type_key].append(source)
target.update(value_to_change)
try:
exec("target_dictionary{}.update({})".format(path_to_adjust, target))
except:
# Yes I know, this is against PEP8.
pass
except KeyError:
pass
|
def change_value_in_dict(target_dictionary, path_to_change, value_to_change):
if type(path_to_change) is str:
path_to_change = path_to_change.split(".")
if type(path_to_change) is not list:
return False
path_to_adjust = '["{}"]'.format('"]["'.join(path_to_change))
try:
target = eval("target_dictionary{}".format(path_to_adjust))
for key, value in value_to_change.items():
if "type" in value:
type_key = value["type"]
source = value
source["referenced_name"] = key
if type_key not in target:
target[type_key] = list()
elif type_key in target and type(target[type_key]) is not list:
target[type_key] = [target[type_key]]
target[type_key].append(source)
target.update(value_to_change)
try:
exec("target_dictionary{}.update({})".format(path_to_adjust, target))
except:
# Yes I know, this is against PEP8.
pass
except KeyError:
pass
|
https://github.com/terraform-compliance/cli/issues/53
|
terraform-compliance v0.4.11 initiated
Steps : /usr/local/lib/python2.7/site-packages/terraform_compliance/steps
Features : /Users/demianginther/git/tf-modules/compliance
TF Files : /var/folders/zf/f1h382nn35z3gd1kv92bw6r80000gn/T/tmpxTN1V9 (.)
Reading terraform files.
All HCL files look good.
Running tests.
Feature: Resources should be properly tagged # /Users/demianginther/git/tf-modules/compliance/tags.feature
In order to keep track of resource ownership
As engineers
We'll enforce tagging on all resources
1 features (0 passed)
1 scenarios (0 passed)
3 steps (0 passed)
Run 1547251063 finished within a moment
Error: Hook 'load_terraform_data' from /usr/local/lib/python2.7/site-packages/terraform_compliance/steps/terrain.py:6 raised: 'SyntaxError: invalid syntax (<string>, line 1)'
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/radish/hookregistry.py", line 121, in call
func(model, *args, **kwargs)
File "/usr/local/lib/python2.7/site-packages/terraform_compliance/steps/terrain.py", line 12, in load_terraform_data
enable_resource_mounting(tf_conf.terraform_config)
File "/usr/local/lib/python2.7/site-packages/terraform_compliance/extensions/terraform_validate.py", line 29, in enable_resource_mounting
enable_resource_mounting(tf_conf, sub_value, sub_resource)
File "/usr/local/lib/python2.7/site-packages/terraform_compliance/extensions/terraform_validate.py", line 29, in enable_resource_mounting
enable_resource_mounting(tf_conf, sub_value, sub_resource)
File "/usr/local/lib/python2.7/site-packages/terraform_compliance/extensions/terraform_validate.py", line 37, in enable_resource_mounting
change_value_in_dict(tf_conf, target, {source: processing_resource})
File "/usr/local/lib/python2.7/site-packages/terraform_compliance/common/helper.py", line 119, in change_value_in_dict
target = eval('target_dictionary{}'.format(path_to_adjust))
File "<string>", line 1
target_dictionary["resource"]["!var"]["alb_enabled && !var"]["double_elb_listener_enabled && var"]["env == "prod" ? 1 : 0"]
^
SyntaxError: invalid syntax
|
SyntaxError
|
def make_statements(code, variables, dtype, optimise=True, blockname=""):
"""
make_statements(code, variables, dtype, optimise=True, blockname='')
Turn a series of abstract code statements into Statement objects, inferring
whether each line is a set/declare operation, whether the variables are
constant or not, and handling the cacheing of subexpressions.
Parameters
----------
code : str
A (multi-line) string of statements.
variables : dict-like
A dictionary of with `Variable` and `Function` objects for every
identifier used in the `code`.
dtype : `dtype`
The data type to use for temporary variables
optimise : bool, optional
Whether to optimise expressions, including
pulling out loop invariant expressions and putting them in new
scalar constants. Defaults to ``False``, since this function is also
used just to in contexts where we are not interested by this kind of
optimisation. For the main code generation stage, its value is set by
the `codegen.loop_invariant_optimisations` preference.
blockname : str, optional
A name for the block (used to name intermediate variables to avoid
name clashes when multiple blocks are used together)
Returns
-------
scalar_statements, vector_statements : (list of `Statement`, list of `Statement`)
Lists with statements that are to be executed once and statements that
are to be executed once for every neuron/synapse/... (or in a vectorised
way)
Notes
-----
If ``optimise`` is ``True``, then the
``scalar_statements`` may include newly introduced scalar constants that
have been identified as loop-invariant and have therefore been pulled out
of the vector statements. The resulting statements will also use augmented
assignments where possible, i.e. a statement such as ``w = w + 1`` will be
replaced by ``w += 1``. Also, statements involving booleans will have
additional information added to them (see `Statement` for details)
describing how the statement can be reformulated as a sequence of if/then
statements. Calls `~brian2.codegen.optimisation.optimise_statements`.
"""
code = strip_empty_lines(deindent(code))
lines = re.split(r"[;\n]", code)
lines = [LineInfo(code=line) for line in lines if len(line)]
# Do a copy so we can add stuff without altering the original dict
variables = dict(variables)
# we will do inference to work out which lines are := and which are =
defined = set(
k for k, v in variables.items() if not isinstance(v, AuxiliaryVariable)
)
for line in lines:
statement = None
# parse statement into "var op expr"
var, op, expr, comment = parse_statement(line.code)
if var in variables and isinstance(variables[var], Subexpression):
raise SyntaxError(
"Illegal line '{line}' in abstract code. "
"Cannot write to subexpression "
"'{var}'.".format(line=line.code, var=var)
)
if op == "=":
if var not in defined:
op = ":="
defined.add(var)
if var not in variables:
annotated_ast = brian_ast(expr, variables)
is_scalar = annotated_ast.scalar
if annotated_ast.dtype == "boolean":
use_dtype = bool
elif annotated_ast.dtype == "integer":
use_dtype = int
else:
use_dtype = dtype
new_var = AuxiliaryVariable(var, dtype=use_dtype, scalar=is_scalar)
variables[var] = new_var
elif not variables[var].is_boolean:
sympy_expr = str_to_sympy(expr, variables)
if variables[var].is_integer:
sympy_var = sympy.Symbol(var, integer=True)
else:
sympy_var = sympy.Symbol(var, real=True)
try:
collected = sympy.collect(
sympy_expr, sympy_var, exact=True, evaluate=False
)
except AttributeError:
# If something goes wrong during collection, e.g. collect
# does not work for logical expressions
collected = {1: sympy_expr}
if (
len(collected) == 2
and set(collected.keys()) == {1, sympy_var}
and collected[sympy_var] == 1
):
# We can replace this statement by a += assignment
statement = Statement(
var,
"+=",
sympy_to_str(collected[1]),
comment,
dtype=variables[var].dtype,
scalar=variables[var].scalar,
)
elif len(collected) == 1 and sympy_var in collected:
# We can replace this statement by a *= assignment
statement = Statement(
var,
"*=",
sympy_to_str(collected[sympy_var]),
comment,
dtype=variables[var].dtype,
scalar=variables[var].scalar,
)
if statement is None:
statement = Statement(
var,
op,
expr,
comment,
dtype=variables[var].dtype,
scalar=variables[var].scalar,
)
line.statement = statement
# for each line will give the variable being written to
line.write = var
# each line will give a set of variables which are read
line.read = get_identifiers_recursively([expr], variables)
# All writes to scalar variables must happen before writes to vector
# variables
scalar_write_done = False
for line in lines:
stmt = line.statement
if stmt.op != ":=" and variables[stmt.var].scalar and scalar_write_done:
raise SyntaxError(
(
"All writes to scalar variables in a code block "
"have to be made before writes to vector "
"variables. Illegal write to %s."
)
% line.write
)
elif not variables[stmt.var].scalar:
scalar_write_done = True
# all variables which are written to at some point in the code block
# used to determine whether they should be const or not
all_write = set(line.write for line in lines)
# backwards compute whether or not variables will be read again
# note that will_read for a line gives the set of variables it will read
# on the current line or subsequent ones. will_write gives the set of
# variables that will be written after the current line
will_read = set()
will_write = set()
for line in lines[::-1]:
will_read = will_read.union(line.read)
line.will_read = will_read.copy()
line.will_write = will_write.copy()
will_write.add(line.write)
subexpressions = dict(
(name, val) for name, val in variables.items() if isinstance(val, Subexpression)
)
# Check that no scalar subexpression refers to a vectorised function
# (e.g. rand()) -- otherwise it would be differently interpreted depending
# on whether it is used in a scalar or a vector context (i.e., even though
# the subexpression is supposed to be scalar, it would be vectorised when
# used as part of non-scalar expressions)
for name, subexpr in subexpressions.items():
if subexpr.scalar:
identifiers = get_identifiers(subexpr.expr)
for identifier in identifiers:
if identifier in variables and getattr(
variables[identifier], "auto_vectorise", False
):
raise SyntaxError(
(
"The scalar subexpression {} refers to "
"the implicitly vectorised function {} "
"-- this is not allowed since it leads "
"to different interpretations of this "
"subexpression depending on whether it "
"is used in a scalar or vector "
"context."
).format(name, identifier)
)
# sort subexpressions into an order so that subexpressions that don't depend
# on other subexpressions are first
subexpr_deps = dict(
(name, [dep for dep in subexpr.identifiers if dep in subexpressions])
for name, subexpr in subexpressions.items()
)
sorted_subexpr_vars = topsort(subexpr_deps)
statements = []
# none are yet defined (or declared)
subdefined = dict((name, None) for name in subexpressions)
for line in lines:
stmt = line.statement
read = line.read
write = line.write
will_read = line.will_read
will_write = line.will_write
# update/define all subexpressions needed by this statement
for var in sorted_subexpr_vars:
if var not in read:
continue
subexpression = subexpressions[var]
# if already defined/declared
if subdefined[var] == "constant":
continue
elif subdefined[var] == "variable":
op = "="
constant = False
else:
op = ":="
# check if the referred variables ever change
ids = subexpression.identifiers
constant = all(v not in will_write for v in ids)
subdefined[var] = "constant" if constant else "variable"
statement = Statement(
var,
op,
subexpression.expr,
comment="",
dtype=variables[var].dtype,
constant=constant,
subexpression=True,
scalar=variables[var].scalar,
)
statements.append(statement)
var, op, expr, comment = stmt.var, stmt.op, stmt.expr, stmt.comment
# constant only if we are declaring a new variable and we will not
# write to it again
constant = op == ":=" and var not in will_write
statement = Statement(
var,
op,
expr,
comment,
dtype=variables[var].dtype,
constant=constant,
scalar=variables[var].scalar,
)
statements.append(statement)
scalar_statements = [s for s in statements if s.scalar]
vector_statements = [s for s in statements if not s.scalar]
if optimise and prefs.codegen.loop_invariant_optimisations:
scalar_statements, vector_statements = optimise_statements(
scalar_statements, vector_statements, variables, blockname=blockname
)
return scalar_statements, vector_statements
|
def make_statements(code, variables, dtype, optimise=True, blockname=""):
"""
make_statements(code, variables, dtype, optimise=True, blockname='')
Turn a series of abstract code statements into Statement objects, inferring
whether each line is a set/declare operation, whether the variables are
constant or not, and handling the cacheing of subexpressions.
Parameters
----------
code : str
A (multi-line) string of statements.
variables : dict-like
A dictionary of with `Variable` and `Function` objects for every
identifier used in the `code`.
dtype : `dtype`
The data type to use for temporary variables
optimise : bool, optional
Whether to optimise expressions, including
pulling out loop invariant expressions and putting them in new
scalar constants. Defaults to ``False``, since this function is also
used just to in contexts where we are not interested by this kind of
optimisation. For the main code generation stage, its value is set by
the `codegen.loop_invariant_optimisations` preference.
blockname : str, optional
A name for the block (used to name intermediate variables to avoid
name clashes when multiple blocks are used together)
Returns
-------
scalar_statements, vector_statements : (list of `Statement`, list of `Statement`)
Lists with statements that are to be executed once and statements that
are to be executed once for every neuron/synapse/... (or in a vectorised
way)
Notes
-----
If ``optimise`` is ``True``, then the
``scalar_statements`` may include newly introduced scalar constants that
have been identified as loop-invariant and have therefore been pulled out
of the vector statements. The resulting statements will also use augmented
assignments where possible, i.e. a statement such as ``w = w + 1`` will be
replaced by ``w += 1``. Also, statements involving booleans will have
additional information added to them (see `Statement` for details)
describing how the statement can be reformulated as a sequence of if/then
statements. Calls `~brian2.codegen.optimisation.optimise_statements`.
"""
code = strip_empty_lines(deindent(code))
lines = re.split(r"[;\n]", code)
lines = [LineInfo(code=line) for line in lines if len(line)]
# Do a copy so we can add stuff without altering the original dict
variables = dict(variables)
# we will do inference to work out which lines are := and which are =
defined = set(
k for k, v in variables.items() if not isinstance(v, AuxiliaryVariable)
)
for line in lines:
statement = None
# parse statement into "var op expr"
var, op, expr, comment = parse_statement(line.code)
if var in variables and isinstance(variables[var], Subexpression):
raise SyntaxError(
"Illegal line '{line}' in abstract code. "
"Cannot write to subexpression "
"'{var}'.".format(line=line.code, var=var)
)
if op == "=":
if var not in defined:
op = ":="
defined.add(var)
if var not in variables:
annotated_ast = brian_ast(expr, variables)
is_scalar = annotated_ast.scalar
if annotated_ast.dtype == "boolean":
use_dtype = bool
elif annotated_ast.dtype == "integer":
use_dtype = int
else:
use_dtype = dtype
new_var = AuxiliaryVariable(var, dtype=use_dtype, scalar=is_scalar)
variables[var] = new_var
elif not variables[var].is_boolean:
sympy_expr = str_to_sympy(expr, variables)
sympy_var = sympy.Symbol(var, real=True)
try:
collected = sympy.collect(
sympy_expr, sympy_var, exact=True, evaluate=False
)
except AttributeError:
# If something goes wrong during collection, e.g. collect
# does not work for logical expressions
collected = {1: sympy_expr}
if (
len(collected) == 2
and set(collected.keys()) == {1, sympy_var}
and collected[sympy_var] == 1
):
# We can replace this statement by a += assignment
statement = Statement(
var,
"+=",
sympy_to_str(collected[1]),
comment,
dtype=variables[var].dtype,
scalar=variables[var].scalar,
)
elif len(collected) == 1 and sympy_var in collected:
# We can replace this statement by a *= assignment
statement = Statement(
var,
"*=",
sympy_to_str(collected[sympy_var]),
comment,
dtype=variables[var].dtype,
scalar=variables[var].scalar,
)
if statement is None:
statement = Statement(
var,
op,
expr,
comment,
dtype=variables[var].dtype,
scalar=variables[var].scalar,
)
line.statement = statement
# for each line will give the variable being written to
line.write = var
# each line will give a set of variables which are read
line.read = get_identifiers_recursively([expr], variables)
# All writes to scalar variables must happen before writes to vector
# variables
scalar_write_done = False
for line in lines:
stmt = line.statement
if stmt.op != ":=" and variables[stmt.var].scalar and scalar_write_done:
raise SyntaxError(
(
"All writes to scalar variables in a code block "
"have to be made before writes to vector "
"variables. Illegal write to %s."
)
% line.write
)
elif not variables[stmt.var].scalar:
scalar_write_done = True
# all variables which are written to at some point in the code block
# used to determine whether they should be const or not
all_write = set(line.write for line in lines)
# backwards compute whether or not variables will be read again
# note that will_read for a line gives the set of variables it will read
# on the current line or subsequent ones. will_write gives the set of
# variables that will be written after the current line
will_read = set()
will_write = set()
for line in lines[::-1]:
will_read = will_read.union(line.read)
line.will_read = will_read.copy()
line.will_write = will_write.copy()
will_write.add(line.write)
subexpressions = dict(
(name, val) for name, val in variables.items() if isinstance(val, Subexpression)
)
# Check that no scalar subexpression refers to a vectorised function
# (e.g. rand()) -- otherwise it would be differently interpreted depending
# on whether it is used in a scalar or a vector context (i.e., even though
# the subexpression is supposed to be scalar, it would be vectorised when
# used as part of non-scalar expressions)
for name, subexpr in subexpressions.items():
if subexpr.scalar:
identifiers = get_identifiers(subexpr.expr)
for identifier in identifiers:
if identifier in variables and getattr(
variables[identifier], "auto_vectorise", False
):
raise SyntaxError(
(
"The scalar subexpression {} refers to "
"the implicitly vectorised function {} "
"-- this is not allowed since it leads "
"to different interpretations of this "
"subexpression depending on whether it "
"is used in a scalar or vector "
"context."
).format(name, identifier)
)
# sort subexpressions into an order so that subexpressions that don't depend
# on other subexpressions are first
subexpr_deps = dict(
(name, [dep for dep in subexpr.identifiers if dep in subexpressions])
for name, subexpr in subexpressions.items()
)
sorted_subexpr_vars = topsort(subexpr_deps)
statements = []
# none are yet defined (or declared)
subdefined = dict((name, None) for name in subexpressions)
for line in lines:
stmt = line.statement
read = line.read
write = line.write
will_read = line.will_read
will_write = line.will_write
# update/define all subexpressions needed by this statement
for var in sorted_subexpr_vars:
if var not in read:
continue
subexpression = subexpressions[var]
# if already defined/declared
if subdefined[var] == "constant":
continue
elif subdefined[var] == "variable":
op = "="
constant = False
else:
op = ":="
# check if the referred variables ever change
ids = subexpression.identifiers
constant = all(v not in will_write for v in ids)
subdefined[var] = "constant" if constant else "variable"
statement = Statement(
var,
op,
subexpression.expr,
comment="",
dtype=variables[var].dtype,
constant=constant,
subexpression=True,
scalar=variables[var].scalar,
)
statements.append(statement)
var, op, expr, comment = stmt.var, stmt.op, stmt.expr, stmt.comment
# constant only if we are declaring a new variable and we will not
# write to it again
constant = op == ":=" and var not in will_write
statement = Statement(
var,
op,
expr,
comment,
dtype=variables[var].dtype,
constant=constant,
scalar=variables[var].scalar,
)
statements.append(statement)
scalar_statements = [s for s in statements if s.scalar]
vector_statements = [s for s in statements if not s.scalar]
if optimise and prefs.codegen.loop_invariant_optimisations:
scalar_statements, vector_statements = optimise_statements(
scalar_statements, vector_statements, variables, blockname=blockname
)
return scalar_statements, vector_statements
|
https://github.com/brian-team/brian2/issues/1199
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/codegen/runtime/numpy_rt/numpy_rt.py", line 246, in run
exec(self.compiled_code, self.namespace)
File "(string)", line 19, in <module>
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/input/timedarray.py", line 230, in unitless_timed_array_func
return values[timestep, i]
IndexError: arrays used as indices must be of integer (or boolean) type
Error encountered with object named "neurongroup".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-6-321ca0774a4a>", line 18, in <module>
method='euler')
An exception occured during the execution of code object neurongroup_stateupdater_codeobject.
The error was raised in the following line:
_v = (_lio_1 * I(t, 2.0 + i)) + v
IndexError: arrays used as indices must be of integer (or boolean) type
(See above for original error message and traceback.)
|
IndexError
|
def get_substituted_expressions(self, variables=None, include_subexpressions=False):
"""
Return a list of ``(varname, expr)`` tuples, containing all
differential equations (and optionally subexpressions) with all the
subexpression variables substituted with the respective expressions.
Parameters
----------
variables : dict, optional
A mapping of variable names to `Variable`/`Function` objects.
include_subexpressions : bool
Whether also to return substituted subexpressions. Defaults to
``False``.
Returns
-------
expr_tuples : list of (str, `CodeString`)
A list of ``(varname, expr)`` tuples, where ``expr`` is a
`CodeString` object with all subexpression variables substituted
with the respective expression.
"""
if self._substituted_expressions is None:
self._substituted_expressions = []
substitutions = {}
for eq in self.ordered:
# Skip parameters
if eq.expr is None:
continue
new_sympy_expr = str_to_sympy(eq.expr.code, variables).xreplace(
substitutions
)
new_str_expr = sympy_to_str(new_sympy_expr)
expr = Expression(new_str_expr)
if eq.type == SUBEXPRESSION:
if eq.var_type == INTEGER:
sympy_var = sympy.Symbol(eq.varname, integer=True)
else:
sympy_var = sympy.Symbol(eq.varname, real=True)
substitutions.update({sympy_var: str_to_sympy(expr.code, variables)})
self._substituted_expressions.append((eq.varname, expr))
elif eq.type == DIFFERENTIAL_EQUATION:
# a differential equation that we have to check
self._substituted_expressions.append((eq.varname, expr))
else:
raise AssertionError("Unknown equation type %s" % eq.type)
if include_subexpressions:
return self._substituted_expressions
else:
return [
(name, expr)
for name, expr in self._substituted_expressions
if self[name].type == DIFFERENTIAL_EQUATION
]
|
def get_substituted_expressions(self, variables=None, include_subexpressions=False):
"""
Return a list of ``(varname, expr)`` tuples, containing all
differential equations (and optionally subexpressions) with all the
subexpression variables substituted with the respective expressions.
Parameters
----------
variables : dict, optional
A mapping of variable names to `Variable`/`Function` objects.
include_subexpressions : bool
Whether also to return substituted subexpressions. Defaults to
``False``.
Returns
-------
expr_tuples : list of (str, `CodeString`)
A list of ``(varname, expr)`` tuples, where ``expr`` is a
`CodeString` object with all subexpression variables substituted
with the respective expression.
"""
if self._substituted_expressions is None:
self._substituted_expressions = []
substitutions = {}
for eq in self.ordered:
# Skip parameters
if eq.expr is None:
continue
new_sympy_expr = str_to_sympy(eq.expr.code, variables).xreplace(
substitutions
)
new_str_expr = sympy_to_str(new_sympy_expr)
expr = Expression(new_str_expr)
if eq.type == SUBEXPRESSION:
substitutions.update(
{
sympy.Symbol(eq.varname, real=True): str_to_sympy(
expr.code, variables
)
}
)
self._substituted_expressions.append((eq.varname, expr))
elif eq.type == DIFFERENTIAL_EQUATION:
# a differential equation that we have to check
self._substituted_expressions.append((eq.varname, expr))
else:
raise AssertionError("Unknown equation type %s" % eq.type)
if include_subexpressions:
return self._substituted_expressions
else:
return [
(name, expr)
for name, expr in self._substituted_expressions
if self[name].type == DIFFERENTIAL_EQUATION
]
|
https://github.com/brian-team/brian2/issues/1199
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/codegen/runtime/numpy_rt/numpy_rt.py", line 246, in run
exec(self.compiled_code, self.namespace)
File "(string)", line 19, in <module>
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/input/timedarray.py", line 230, in unitless_timed_array_func
return values[timestep, i]
IndexError: arrays used as indices must be of integer (or boolean) type
Error encountered with object named "neurongroup".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-6-321ca0774a4a>", line 18, in <module>
method='euler')
An exception occured during the execution of code object neurongroup_stateupdater_codeobject.
The error was raised in the following line:
_v = (_lio_1 * I(t, 2.0 + i)) + v
IndexError: arrays used as indices must be of integer (or boolean) type
(See above for original error message and traceback.)
|
IndexError
|
def render_node(self, node):
nodename = node.__class__.__name__
methname = "render_" + nodename
try:
return getattr(self, methname)(node)
except AttributeError:
raise SyntaxError("Unknown syntax: " + nodename)
|
def render_node(self, node):
nodename = node.__class__.__name__
methname = "render_" + nodename
try:
return getattr(self, methname)(node)
except AttributeError:
raise
raise SyntaxError("Unknown syntax: " + nodename)
|
https://github.com/brian-team/brian2/issues/1199
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/codegen/runtime/numpy_rt/numpy_rt.py", line 246, in run
exec(self.compiled_code, self.namespace)
File "(string)", line 19, in <module>
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/input/timedarray.py", line 230, in unitless_timed_array_func
return values[timestep, i]
IndexError: arrays used as indices must be of integer (or boolean) type
Error encountered with object named "neurongroup".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-6-321ca0774a4a>", line 18, in <module>
method='euler')
An exception occured during the execution of code object neurongroup_stateupdater_codeobject.
The error was raised in the following line:
_v = (_lio_1 * I(t, 2.0 + i)) + v
IndexError: arrays used as indices must be of integer (or boolean) type
(See above for original error message and traceback.)
|
IndexError
|
def render_Num(self, node):
if isinstance(node.n, numbers.Integral):
return sympy.Integer(node.n)
else:
return sympy.Float(node.n)
|
def render_Num(self, node):
return sympy.Float(node.n)
|
https://github.com/brian-team/brian2/issues/1199
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/codegen/runtime/numpy_rt/numpy_rt.py", line 246, in run
exec(self.compiled_code, self.namespace)
File "(string)", line 19, in <module>
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/input/timedarray.py", line 230, in unitless_timed_array_func
return values[timestep, i]
IndexError: arrays used as indices must be of integer (or boolean) type
Error encountered with object named "neurongroup".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-6-321ca0774a4a>", line 18, in <module>
method='euler')
An exception occured during the execution of code object neurongroup_stateupdater_codeobject.
The error was raised in the following line:
_v = (_lio_1 * I(t, 2.0 + i)) + v
IndexError: arrays used as indices must be of integer (or boolean) type
(See above for original error message and traceback.)
|
IndexError
|
def __call__(self, eqs, variables=None, method_options=None):
"""
Apply a state updater description to model equations.
Parameters
----------
eqs : `Equations`
The equations describing the model
variables: dict-like, optional
The `Variable` objects for the model. Ignored by the explicit
state updater.
method_options : dict, optional
Additional options to the state updater (not used at the moment
for the explicit state updaters).
Examples
--------
>>> from brian2 import *
>>> eqs = Equations('dv/dt = -v / tau : volt')
>>> print(euler(eqs))
_v = -dt*v/tau + v
v = _v
>>> print(rk4(eqs))
__k_1_v = -dt*v/tau
__k_2_v = -dt*(__k_1_v/2 + v)/tau
__k_3_v = -dt*(__k_2_v/2 + v)/tau
__k_4_v = -dt*(__k_3_v + v)/tau
_v = __k_1_v/6 + __k_2_v/3 + __k_3_v/3 + __k_4_v/6 + v
v = _v
"""
method_options = extract_method_options(method_options, {})
# Non-stochastic numerical integrators should work for all equations,
# except for stochastic equations
if eqs.is_stochastic and self.stochastic is None:
raise UnsupportedEquationsException(
"Cannot integrate stochastic equations with this state updater."
)
if self.custom_check:
self.custom_check(eqs, variables)
# The final list of statements
statements = []
stochastic_variables = eqs.stochastic_variables
# The variables for the intermediate results in the state updater
# description, e.g. the variable k in rk2
intermediate_vars = [var for var, expr in self.statements]
# A dictionary mapping all the variables in the equations to their
# sympy representations
eq_variables = dict(((var, _symbol(var)) for var in eqs.eq_names))
# Generate the random numbers for the stochastic variables
for stochastic_variable in stochastic_variables:
statements.append(stochastic_variable + " = " + "dt**.5 * randn()")
substituted_expressions = eqs.get_substituted_expressions(variables)
# Process the intermediate statements in the stateupdater description
for intermediate_var, intermediate_expr in self.statements:
# Split the expression into a non-stochastic and a stochastic part
non_stochastic_expr, stochastic_expr = split_expression(intermediate_expr)
# Execute the statement by appropriately replacing the functions f
# and g and the variable x for every equation in the model.
# We use the model equations where the subexpressions have
# already been substituted into the model equations.
for var, expr in substituted_expressions:
for xi in stochastic_variables:
RHS = self._generate_RHS(
eqs,
var,
eq_variables,
intermediate_vars,
expr,
non_stochastic_expr,
stochastic_expr,
xi,
)
statements.append(intermediate_var + "_" + var + "_" + xi + " = " + RHS)
if not stochastic_variables: # no stochastic variables
RHS = self._generate_RHS(
eqs,
var,
eq_variables,
intermediate_vars,
expr,
non_stochastic_expr,
stochastic_expr,
)
statements.append(intermediate_var + "_" + var + " = " + RHS)
# Process the "return" line of the stateupdater description
non_stochastic_expr, stochastic_expr = split_expression(self.output)
if eqs.is_stochastic and (
self.stochastic != "multiplicative" and eqs.stochastic_type == "multiplicative"
):
# The equations are marked as having multiplicative noise and the
# current state updater does not support such equations. However,
# it is possible that the equations do not use multiplicative noise
# at all. They could depend on time via a function that is constant
# over a single time step (most likely, a TimedArray). In that case
# we can integrate the equations
dt_value = variables["dt"].get_value()[0] if "dt" in variables else None
for _, expr in substituted_expressions:
_, stoch = expr.split_stochastic()
if stoch is None:
continue
# There could be more than one stochastic variable (e.g. xi_1, xi_2)
for _, stoch_expr in stoch.items():
sympy_expr = str_to_sympy(stoch_expr.code)
# The equation really has multiplicative noise, if it depends
# on time (and not only via a function that is constant
# over dt), or if it depends on another variable defined
# via differential equations.
if not is_constant_over_dt(sympy_expr, variables, dt_value) or len(
stoch_expr.identifiers & eqs.diff_eq_names
):
raise UnsupportedEquationsException(
"Cannot integrate "
"equations with "
"multiplicative noise with "
"this state updater."
)
# Assign a value to all the model variables described by differential
# equations
for var, expr in substituted_expressions:
RHS = self._generate_RHS(
eqs,
var,
eq_variables,
intermediate_vars,
expr,
non_stochastic_expr,
stochastic_expr,
stochastic_variables,
)
statements.append("_" + var + " = " + RHS)
# Assign everything to the final variables
for var, expr in substituted_expressions:
statements.append(var + " = " + "_" + var)
return "\n".join(statements)
|
def __call__(self, eqs, variables=None, method_options=None):
"""
Apply a state updater description to model equations.
Parameters
----------
eqs : `Equations`
The equations describing the model
variables: dict-like, optional
The `Variable` objects for the model. Ignored by the explicit
state updater.
method_options : dict, optional
Additional options to the state updater (not used at the moment
for the explicit state updaters).
Examples
--------
>>> from brian2 import *
>>> eqs = Equations('dv/dt = -v / tau : volt')
>>> print(euler(eqs))
_v = -dt*v/tau + v
v = _v
>>> print(rk4(eqs))
__k_1_v = -dt*v/tau
__k_2_v = -dt*(0.5*__k_1_v + v)/tau
__k_3_v = -dt*(0.5*__k_2_v + v)/tau
__k_4_v = -dt*(__k_3_v + v)/tau
_v = 0.166666666666667*__k_1_v + 0.333333333333333*__k_2_v + 0.333333333333333*__k_3_v + 0.166666666666667*__k_4_v + v
v = _v
"""
method_options = extract_method_options(method_options, {})
# Non-stochastic numerical integrators should work for all equations,
# except for stochastic equations
if eqs.is_stochastic and self.stochastic is None:
raise UnsupportedEquationsException(
"Cannot integrate stochastic equations with this state updater."
)
if self.custom_check:
self.custom_check(eqs, variables)
# The final list of statements
statements = []
stochastic_variables = eqs.stochastic_variables
# The variables for the intermediate results in the state updater
# description, e.g. the variable k in rk2
intermediate_vars = [var for var, expr in self.statements]
# A dictionary mapping all the variables in the equations to their
# sympy representations
eq_variables = dict(((var, _symbol(var)) for var in eqs.eq_names))
# Generate the random numbers for the stochastic variables
for stochastic_variable in stochastic_variables:
statements.append(stochastic_variable + " = " + "dt**.5 * randn()")
substituted_expressions = eqs.get_substituted_expressions(variables)
# Process the intermediate statements in the stateupdater description
for intermediate_var, intermediate_expr in self.statements:
# Split the expression into a non-stochastic and a stochastic part
non_stochastic_expr, stochastic_expr = split_expression(intermediate_expr)
# Execute the statement by appropriately replacing the functions f
# and g and the variable x for every equation in the model.
# We use the model equations where the subexpressions have
# already been substituted into the model equations.
for var, expr in substituted_expressions:
for xi in stochastic_variables:
RHS = self._generate_RHS(
eqs,
var,
eq_variables,
intermediate_vars,
expr,
non_stochastic_expr,
stochastic_expr,
xi,
)
statements.append(intermediate_var + "_" + var + "_" + xi + " = " + RHS)
if not stochastic_variables: # no stochastic variables
RHS = self._generate_RHS(
eqs,
var,
eq_variables,
intermediate_vars,
expr,
non_stochastic_expr,
stochastic_expr,
)
statements.append(intermediate_var + "_" + var + " = " + RHS)
# Process the "return" line of the stateupdater description
non_stochastic_expr, stochastic_expr = split_expression(self.output)
if eqs.is_stochastic and (
self.stochastic != "multiplicative" and eqs.stochastic_type == "multiplicative"
):
# The equations are marked as having multiplicative noise and the
# current state updater does not support such equations. However,
# it is possible that the equations do not use multiplicative noise
# at all. They could depend on time via a function that is constant
# over a single time step (most likely, a TimedArray). In that case
# we can integrate the equations
dt_value = variables["dt"].get_value()[0] if "dt" in variables else None
for _, expr in substituted_expressions:
_, stoch = expr.split_stochastic()
if stoch is None:
continue
# There could be more than one stochastic variable (e.g. xi_1, xi_2)
for _, stoch_expr in stoch.items():
sympy_expr = str_to_sympy(stoch_expr.code)
# The equation really has multiplicative noise, if it depends
# on time (and not only via a function that is constant
# over dt), or if it depends on another variable defined
# via differential equations.
if not is_constant_over_dt(sympy_expr, variables, dt_value) or len(
stoch_expr.identifiers & eqs.diff_eq_names
):
raise UnsupportedEquationsException(
"Cannot integrate "
"equations with "
"multiplicative noise with "
"this state updater."
)
# Assign a value to all the model variables described by differential
# equations
for var, expr in substituted_expressions:
RHS = self._generate_RHS(
eqs,
var,
eq_variables,
intermediate_vars,
expr,
non_stochastic_expr,
stochastic_expr,
stochastic_variables,
)
statements.append("_" + var + " = " + RHS)
# Assign everything to the final variables
for var, expr in substituted_expressions:
statements.append(var + " = " + "_" + var)
return "\n".join(statements)
|
https://github.com/brian-team/brian2/issues/1199
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/codegen/runtime/numpy_rt/numpy_rt.py", line 246, in run
exec(self.compiled_code, self.namespace)
File "(string)", line 19, in <module>
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/input/timedarray.py", line 230, in unitless_timed_array_func
return values[timestep, i]
IndexError: arrays used as indices must be of integer (or boolean) type
Error encountered with object named "neurongroup".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-6-321ca0774a4a>", line 18, in <module>
method='euler')
An exception occured during the execution of code object neurongroup_stateupdater_codeobject.
The error was raised in the following line:
_v = (_lio_1 * I(t, 2.0 + i)) + v
IndexError: arrays used as indices must be of integer (or boolean) type
(See above for original error message and traceback.)
|
IndexError
|
def get_conditionally_linear_system(eqs, variables=None):
'''
Convert equations into a linear system using sympy.
Parameters
----------
eqs : `Equations`
The model equations.
Returns
-------
coefficients : dict of (sympy expression, sympy expression) tuples
For every variable x, a tuple (M, B) containing the coefficients M and
B (as sympy expressions) for M * x + B
Raises
------
ValueError
If one of the equations cannot be converted into a M * x + B form.
Examples
--------
>>> from brian2 import Equations
>>> eqs = Equations("""
... dv/dt = (-v + w**2.0) / tau : 1
... dw/dt = -w / tau : 1
... """)
>>> system = get_conditionally_linear_system(eqs)
>>> print(system['v'])
(-1/tau, w**2.0/tau)
>>> print(system['w'])
(-1/tau, 0)
'''
diff_eqs = eqs.get_substituted_expressions(variables)
coefficients = {}
for name, expr in diff_eqs:
var = sp.Symbol(name, real=True)
s_expr = str_to_sympy(expr.code, variables).expand()
if s_expr.has(var):
# Factor out the variable
s_expr = sp.collect(s_expr, var, evaluate=False)
if len(s_expr) > 2 or var not in s_expr:
raise ValueError(
(
'The expression "%s", defining the variable %s, '
"could not be separated into linear components"
)
% (expr, name)
)
coefficients[name] = (s_expr[var], s_expr.get(1, 0))
else:
coefficients[name] = (0, s_expr)
return coefficients
|
def get_conditionally_linear_system(eqs, variables=None):
'''
Convert equations into a linear system using sympy.
Parameters
----------
eqs : `Equations`
The model equations.
Returns
-------
coefficients : dict of (sympy expression, sympy expression) tuples
For every variable x, a tuple (M, B) containing the coefficients M and
B (as sympy expressions) for M * x + B
Raises
------
ValueError
If one of the equations cannot be converted into a M * x + B form.
Examples
--------
>>> from brian2 import Equations
>>> eqs = Equations("""
... dv/dt = (-v + w**2) / tau : 1
... dw/dt = -w / tau : 1
... """)
>>> system = get_conditionally_linear_system(eqs)
>>> print(system['v'])
(-1/tau, w**2.0/tau)
>>> print(system['w'])
(-1/tau, 0)
'''
diff_eqs = eqs.get_substituted_expressions(variables)
coefficients = {}
for name, expr in diff_eqs:
var = sp.Symbol(name, real=True)
s_expr = str_to_sympy(expr.code, variables).expand()
if s_expr.has(var):
# Factor out the variable
s_expr = sp.collect(s_expr, var, evaluate=False)
if len(s_expr) > 2 or var not in s_expr:
raise ValueError(
(
'The expression "%s", defining the variable %s, '
"could not be separated into linear components"
)
% (expr, name)
)
coefficients[name] = (s_expr[var], s_expr.get(1, 0))
else:
coefficients[name] = (0, s_expr)
return coefficients
|
https://github.com/brian-team/brian2/issues/1199
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/codegen/runtime/numpy_rt/numpy_rt.py", line 246, in run
exec(self.compiled_code, self.namespace)
File "(string)", line 19, in <module>
File "miniconda2/envs/brian/lib/python2.7/site-packages/brian2/input/timedarray.py", line 230, in unitless_timed_array_func
return values[timestep, i]
IndexError: arrays used as indices must be of integer (or boolean) type
Error encountered with object named "neurongroup".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-6-321ca0774a4a>", line 18, in <module>
method='euler')
An exception occured during the execution of code object neurongroup_stateupdater_codeobject.
The error was raised in the following line:
_v = (_lio_1 * I(t, 2.0 + i)) + v
IndexError: arrays used as indices must be of integer (or boolean) type
(See above for original error message and traceback.)
|
IndexError
|
def __init__(self):
super(CPPStandaloneDevice, self).__init__()
#: Dictionary mapping `ArrayVariable` objects to their globally
#: unique name
self.arrays = {}
#: Dictionary mapping `ArrayVariable` objects to their value or to
#: ``None`` if the value (potentially) depends on executed code. This
#: mechanism allows to access state variables in standalone mode if
#: their value is known at run time
self.array_cache = {}
#: List of all dynamic arrays
#: Dictionary mapping `DynamicArrayVariable` objects with 1 dimension to
#: their globally unique name
self.dynamic_arrays = {}
#: Dictionary mapping `DynamicArrayVariable` objects with 2 dimensions
#: to their globally unique name
self.dynamic_arrays_2d = {}
#: List of all arrays to be filled with zeros (list of (var, varname) )
self.zero_arrays = []
#: List of all arrays to be filled with numbers (list of
#: (var, varname, start) tuples
self.arange_arrays = []
#: Whether the simulation has been run
self.has_been_run = False
#: Whether a run should trigger a build
self.build_on_run = False
#: build options
self.build_options = None
#: The directory which contains the generated code and results
self.project_dir = None
#: Whether to generate profiling information (stored in an instance
#: variable to be accessible during CodeObject generation)
self.enable_profiling = False
#: CodeObjects that use profiling (users can potentially enable
#: profiling only for a subset of runs)
self.profiled_codeobjects = []
#: Dict of all static saved arrays
self.static_arrays = {}
self.code_objects = {}
self.main_queue = []
self.runfuncs = {}
self.networks = set()
self.static_array_specs = []
self.report_func = ""
self.synapses = []
#: Code lines that have been manually added with `device.insert_code`
#: Dictionary mapping slot names to lists of lines.
#: Note that the main slot is handled separately as part of `main_queue`
self.code_lines = {
"before_start": [],
"after_start": [],
"before_end": [],
"after_end": [],
}
self.clocks = set([])
self.extra_compile_args = []
self.define_macros = []
self.headers = []
self.include_dirs = ["brianlib/randomkit"]
if sys.platform == "win32":
self.include_dirs += [os.path.join(sys.prefix, "Library", "include")]
else:
self.include_dirs += [os.path.join(sys.prefix, "include")]
self.library_dirs = ["brianlib/randomkit"]
if sys.platform == "win32":
self.library_dirs += [os.path.join(sys.prefix, "Library", "Lib")]
else:
self.library_dirs += [os.path.join(sys.prefix, "lib")]
self.runtime_library_dirs = []
if sys.platform.startswith("linux"):
self.runtime_library_dirs += [os.path.join(sys.prefix, "lib")]
self.run_environment_variables = {}
if sys.platform.startswith("darwin"):
if "DYLD_LIBRARY_PATH" in os.environ:
dyld_library_path = (
os.environ["DYLD_LIBRARY_PATH"] + ":" + os.path.join(sys.prefix, "lib")
)
else:
dyld_library_path = os.path.join(sys.prefix, "lib")
self.run_environment_variables["DYLD_LIBRARY_PATH"] = dyld_library_path
self.libraries = []
if sys.platform == "win32":
self.libraries += ["advapi32"]
self.extra_link_args = []
self.writer = None
|
def __init__(self):
super(CPPStandaloneDevice, self).__init__()
#: Dictionary mapping `ArrayVariable` objects to their globally
#: unique name
self.arrays = {}
#: Dictionary mapping `ArrayVariable` objects to their value or to
#: ``None`` if the value (potentially) depends on executed code. This
#: mechanism allows to access state variables in standalone mode if
#: their value is known at run time
self.array_cache = {}
#: List of all dynamic arrays
#: Dictionary mapping `DynamicArrayVariable` objects with 1 dimension to
#: their globally unique name
self.dynamic_arrays = {}
#: Dictionary mapping `DynamicArrayVariable` objects with 2 dimensions
#: to their globally unique name
self.dynamic_arrays_2d = {}
#: List of all arrays to be filled with zeros (list of (var, varname) )
self.zero_arrays = []
#: List of all arrays to be filled with numbers (list of
#: (var, varname, start) tuples
self.arange_arrays = []
#: Whether the simulation has been run
self.has_been_run = False
#: Whether a run should trigger a build
self.build_on_run = False
#: build options
self.build_options = None
#: The directory which contains the generated code and results
self.project_dir = None
#: Whether to generate profiling information (stored in an instance
#: variable to be accessible during CodeObject generation)
self.enable_profiling = False
#: CodeObjects that use profiling (users can potentially enable
#: profiling only for a subset of runs)
self.profiled_codeobjects = []
#: Dict of all static saved arrays
self.static_arrays = {}
self.code_objects = {}
self.main_queue = []
self.runfuncs = {}
self.networks = []
self.net_synapses = []
self.static_array_specs = []
self.report_func = ""
self.synapses = []
#: Code lines that have been manually added with `device.insert_code`
#: Dictionary mapping slot names to lists of lines.
#: Note that the main slot is handled separately as part of `main_queue`
self.code_lines = {
"before_start": [],
"after_start": [],
"before_end": [],
"after_end": [],
}
self.clocks = set([])
self.extra_compile_args = []
self.define_macros = []
self.headers = []
self.include_dirs = ["brianlib/randomkit"]
if sys.platform == "win32":
self.include_dirs += [os.path.join(sys.prefix, "Library", "include")]
else:
self.include_dirs += [os.path.join(sys.prefix, "include")]
self.library_dirs = ["brianlib/randomkit"]
if sys.platform == "win32":
self.library_dirs += [os.path.join(sys.prefix, "Library", "Lib")]
else:
self.library_dirs += [os.path.join(sys.prefix, "lib")]
self.runtime_library_dirs = []
if sys.platform.startswith("linux"):
self.runtime_library_dirs += [os.path.join(sys.prefix, "lib")]
self.run_environment_variables = {}
if sys.platform.startswith("darwin"):
if "DYLD_LIBRARY_PATH" in os.environ:
dyld_library_path = (
os.environ["DYLD_LIBRARY_PATH"] + ":" + os.path.join(sys.prefix, "lib")
)
else:
dyld_library_path = os.path.join(sys.prefix, "lib")
self.run_environment_variables["DYLD_LIBRARY_PATH"] = dyld_library_path
self.libraries = []
if sys.platform == "win32":
self.libraries += ["advapi32"]
self.extra_link_args = []
self.writer = None
|
https://github.com/brian-team/brian2/issues/1189
|
ERROR Brian 2 encountered an unexpected error. If you think this is bug in Brian 2, please report this issue either to the mailing list at <http://groups.google.com/group/brian-development/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_debug_1uynejn5.log Additionally, you can also include a copy of the script that was run, available at: /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_script_m_84dmg4.py You can also include a copy of the redirected std stream outputs, available at /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_stdout_d2yd1ugv.log and /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_stderr_xkxqltw0.log Thanks! [brian2]
Traceback (most recent call last):
File "/Users/fpbatta/src/assembly_sequences/scripts/run_simulation_simple.py", line 69, in <module>
nn1 = network_sim()
File "/Users/fpbatta/src/assembly_sequences/scripts/run_simulation_simple.py", line 59, in network_sim
bb.get_device().build(directory='PETH_standalone', compile=True, run=True, debug=False)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/device.py", line 1265, in build
self.generate_objects_source(self.writer, self.arange_arrays,
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/device.py", line 633, in generate_objects_source
arr_tmp = self.code_object_class().templater.objects(
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/codegen/templates.py", line 210, in __call__
return MultiTemplate(module)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/codegen/templates.py", line 226, in __init__
s = autoindent_postfilter(str(f()))
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 675, in __call__
return self._invoke(arguments, autoescape)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 679, in _invoke
rv = self._func(*arguments)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/templates/objects.cpp", line 122, in macro
if(f{{name}}.is_open())
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 747, in _fail_with_undefined_error
raise self._undefined_exception(self._undefined_message)
jinja2.exceptions.UndefinedError: dict object has no element <DynamicArrayVariable(dimensions=Dimension(), dtype=int32, scalar=False, constant=True, read_only=True)>
|
jinja2.exceptions.UndefinedError
|
def build(
self,
directory="output",
compile=True,
run=True,
debug=False,
clean=False,
with_output=True,
additional_source_files=None,
run_args=None,
direct_call=True,
**kwds,
):
"""
Build the project
TODO: more details
Parameters
----------
directory : str, optional
The output directory to write the project to, any existing files
will be overwritten. If the given directory name is ``None``, then
a temporary directory will be used (used in the test suite to avoid
problems when running several tests in parallel). Defaults to
``'output'``.
compile : bool, optional
Whether or not to attempt to compile the project. Defaults to
``True``.
run : bool, optional
Whether or not to attempt to run the built project if it
successfully builds. Defaults to ``True``.
debug : bool, optional
Whether to compile in debug mode. Defaults to ``False``.
with_output : bool, optional
Whether or not to show the ``stdout`` of the built program when run.
Output will be shown in case of compilation or runtime error.
Defaults to ``True``.
clean : bool, optional
Whether or not to clean the project before building. Defaults to
``False``.
additional_source_files : list of str, optional
A list of additional ``.cpp`` files to include in the build.
direct_call : bool, optional
Whether this function was called directly. Is used internally to
distinguish an automatic build due to the ``build_on_run`` option
from a manual ``device.build`` call.
"""
if self.build_on_run and direct_call:
raise RuntimeError(
"You used set_device with build_on_run=True "
"(the default option), which will automatically "
"build the simulation at the first encountered "
"run call - do not call device.build manually "
"in this case. If you want to call it manually, "
"e.g. because you have multiple run calls, use "
"set_device with build_on_run=False."
)
if self.has_been_run:
raise RuntimeError(
"The network has already been built and run "
"before. To build several simulations in "
'the same script, call "device.reinit()" '
'and "device.activate()". Note that you '
"will have to set build options (e.g. the "
"directory) and defaultclock.dt again."
)
renames = {
"project_dir": "directory",
"compile_project": "compile",
"run_project": "run",
}
if len(kwds):
msg = ""
for kwd in kwds:
if kwd in renames:
msg += ("Keyword argument '%s' has been renamed to '%s'. ") % (
kwd,
renames[kwd],
)
else:
msg += "Unknown keyword argument '%s'. " % kwd
raise TypeError(msg)
if additional_source_files is None:
additional_source_files = []
if run_args is None:
run_args = []
if directory is None:
directory = tempfile.mkdtemp(prefix="brian_standalone_")
self.project_dir = directory
ensure_directory(directory)
# Determine compiler flags and directories
compiler, default_extra_compile_args = get_compiler_and_args()
extra_compile_args = self.extra_compile_args + default_extra_compile_args
extra_link_args = self.extra_link_args + prefs["codegen.cpp.extra_link_args"]
codeobj_define_macros = [
macro
for codeobj in self.code_objects.values()
for macro in codeobj.compiler_kwds.get("define_macros", [])
]
define_macros = (
self.define_macros + prefs["codegen.cpp.define_macros"] + codeobj_define_macros
)
codeobj_include_dirs = [
include_dir
for codeobj in self.code_objects.values()
for include_dir in codeobj.compiler_kwds.get("include_dirs", [])
]
include_dirs = (
self.include_dirs + prefs["codegen.cpp.include_dirs"] + codeobj_include_dirs
)
codeobj_library_dirs = [
library_dir
for codeobj in self.code_objects.values()
for library_dir in codeobj.compiler_kwds.get("library_dirs", [])
]
library_dirs = (
self.library_dirs + prefs["codegen.cpp.library_dirs"] + codeobj_library_dirs
)
codeobj_runtime_dirs = [
runtime_dir
for codeobj in self.code_objects.values()
for runtime_dir in codeobj.compiler_kwds.get("runtime_library_dirs", [])
]
runtime_library_dirs = (
self.runtime_library_dirs
+ prefs["codegen.cpp.runtime_library_dirs"]
+ codeobj_runtime_dirs
)
codeobj_libraries = [
library
for codeobj in self.code_objects.values()
for library in codeobj.compiler_kwds.get("libraries", [])
]
libraries = self.libraries + prefs["codegen.cpp.libraries"] + codeobj_libraries
compiler_obj = ccompiler.new_compiler(compiler=compiler)
compiler_flags = (
ccompiler.gen_preprocess_options(define_macros, include_dirs)
+ extra_compile_args
)
linker_flags = (
ccompiler.gen_lib_options(
compiler_obj,
library_dirs=library_dirs,
runtime_library_dirs=runtime_library_dirs,
libraries=libraries,
)
+ extra_link_args
)
codeobj_source_files = [
source_file
for codeobj in self.code_objects.values()
for source_file in codeobj.compiler_kwds.get("sources", [])
]
additional_source_files += codeobj_source_files + ["brianlib/randomkit/randomkit.c"]
for d in ["code_objects", "results", "static_arrays"]:
ensure_directory(os.path.join(directory, d))
self.writer = CPPWriter(directory)
# Get the number of threads if specified in an openmp context
nb_threads = prefs.devices.cpp_standalone.openmp_threads
# If the number is negative, we need to throw an error
if nb_threads < 0:
raise ValueError("The number of OpenMP threads can not be negative !")
logger.diagnostic(
"Writing C++ standalone project to directory " + os.path.normpath(directory)
)
self.check_openmp_compatible(nb_threads)
self.write_static_arrays(directory)
# Check that all names are globally unique
names = [obj.name for net in self.networks for obj in net.objects]
non_unique_names = [name for name, count in Counter(names).items() if count > 1]
if len(non_unique_names):
formatted_names = ", ".join("'%s'" % name for name in non_unique_names)
raise ValueError(
"All objects need to have unique names in "
"standalone mode, the following name(s) were used "
"more than once: %s" % formatted_names
)
net_synapses = [
s for net in self.networks for s in net.objects if isinstance(s, Synapses)
]
self.generate_objects_source(
self.writer,
self.arange_arrays,
net_synapses,
self.static_array_specs,
self.networks,
)
self.generate_main_source(self.writer)
self.generate_codeobj_source(self.writer)
self.generate_network_source(self.writer, compiler)
self.generate_synapses_classes_source(self.writer)
self.generate_run_source(self.writer)
self.copy_source_files(self.writer, directory)
self.writer.source_files.extend(additional_source_files)
self.generate_makefile(
self.writer,
compiler,
compiler_flags=" ".join(compiler_flags),
linker_flags=" ".join(linker_flags),
nb_threads=nb_threads,
debug=debug,
)
# Not sure what the best place is to call Network.after_run -- at the
# moment the only important thing it does is to clear the objects stored
# in magic_network. If this is not done, this might lead to problems
# for repeated runs of standalone (e.g. in the test suite).
for net in self.networks:
net.after_run()
if compile:
self.compile_source(directory, compiler, debug, clean)
if run:
self.run(directory, with_output, run_args)
|
def build(
self,
directory="output",
compile=True,
run=True,
debug=False,
clean=False,
with_output=True,
additional_source_files=None,
run_args=None,
direct_call=True,
**kwds,
):
"""
Build the project
TODO: more details
Parameters
----------
directory : str, optional
The output directory to write the project to, any existing files
will be overwritten. If the given directory name is ``None``, then
a temporary directory will be used (used in the test suite to avoid
problems when running several tests in parallel). Defaults to
``'output'``.
compile : bool, optional
Whether or not to attempt to compile the project. Defaults to
``True``.
run : bool, optional
Whether or not to attempt to run the built project if it
successfully builds. Defaults to ``True``.
debug : bool, optional
Whether to compile in debug mode. Defaults to ``False``.
with_output : bool, optional
Whether or not to show the ``stdout`` of the built program when run.
Output will be shown in case of compilation or runtime error.
Defaults to ``True``.
clean : bool, optional
Whether or not to clean the project before building. Defaults to
``False``.
additional_source_files : list of str, optional
A list of additional ``.cpp`` files to include in the build.
direct_call : bool, optional
Whether this function was called directly. Is used internally to
distinguish an automatic build due to the ``build_on_run`` option
from a manual ``device.build`` call.
"""
if self.build_on_run and direct_call:
raise RuntimeError(
"You used set_device with build_on_run=True "
"(the default option), which will automatically "
"build the simulation at the first encountered "
"run call - do not call device.build manually "
"in this case. If you want to call it manually, "
"e.g. because you have multiple run calls, use "
"set_device with build_on_run=False."
)
if self.has_been_run:
raise RuntimeError(
"The network has already been built and run "
"before. To build several simulations in "
'the same script, call "device.reinit()" '
'and "device.activate()". Note that you '
"will have to set build options (e.g. the "
"directory) and defaultclock.dt again."
)
renames = {
"project_dir": "directory",
"compile_project": "compile",
"run_project": "run",
}
if len(kwds):
msg = ""
for kwd in kwds:
if kwd in renames:
msg += ("Keyword argument '%s' has been renamed to '%s'. ") % (
kwd,
renames[kwd],
)
else:
msg += "Unknown keyword argument '%s'. " % kwd
raise TypeError(msg)
if additional_source_files is None:
additional_source_files = []
if run_args is None:
run_args = []
if directory is None:
directory = tempfile.mkdtemp(prefix="brian_standalone_")
self.project_dir = directory
ensure_directory(directory)
# Determine compiler flags and directories
compiler, default_extra_compile_args = get_compiler_and_args()
extra_compile_args = self.extra_compile_args + default_extra_compile_args
extra_link_args = self.extra_link_args + prefs["codegen.cpp.extra_link_args"]
codeobj_define_macros = [
macro
for codeobj in self.code_objects.values()
for macro in codeobj.compiler_kwds.get("define_macros", [])
]
define_macros = (
self.define_macros + prefs["codegen.cpp.define_macros"] + codeobj_define_macros
)
codeobj_include_dirs = [
include_dir
for codeobj in self.code_objects.values()
for include_dir in codeobj.compiler_kwds.get("include_dirs", [])
]
include_dirs = (
self.include_dirs + prefs["codegen.cpp.include_dirs"] + codeobj_include_dirs
)
codeobj_library_dirs = [
library_dir
for codeobj in self.code_objects.values()
for library_dir in codeobj.compiler_kwds.get("library_dirs", [])
]
library_dirs = (
self.library_dirs + prefs["codegen.cpp.library_dirs"] + codeobj_library_dirs
)
codeobj_runtime_dirs = [
runtime_dir
for codeobj in self.code_objects.values()
for runtime_dir in codeobj.compiler_kwds.get("runtime_library_dirs", [])
]
runtime_library_dirs = (
self.runtime_library_dirs
+ prefs["codegen.cpp.runtime_library_dirs"]
+ codeobj_runtime_dirs
)
codeobj_libraries = [
library
for codeobj in self.code_objects.values()
for library in codeobj.compiler_kwds.get("libraries", [])
]
libraries = self.libraries + prefs["codegen.cpp.libraries"] + codeobj_libraries
compiler_obj = ccompiler.new_compiler(compiler=compiler)
compiler_flags = (
ccompiler.gen_preprocess_options(define_macros, include_dirs)
+ extra_compile_args
)
linker_flags = (
ccompiler.gen_lib_options(
compiler_obj,
library_dirs=library_dirs,
runtime_library_dirs=runtime_library_dirs,
libraries=libraries,
)
+ extra_link_args
)
codeobj_source_files = [
source_file
for codeobj in self.code_objects.values()
for source_file in codeobj.compiler_kwds.get("sources", [])
]
additional_source_files += codeobj_source_files + ["brianlib/randomkit/randomkit.c"]
for d in ["code_objects", "results", "static_arrays"]:
ensure_directory(os.path.join(directory, d))
self.writer = CPPWriter(directory)
# Get the number of threads if specified in an openmp context
nb_threads = prefs.devices.cpp_standalone.openmp_threads
# If the number is negative, we need to throw an error
if nb_threads < 0:
raise ValueError("The number of OpenMP threads can not be negative !")
logger.diagnostic(
"Writing C++ standalone project to directory " + os.path.normpath(directory)
)
self.check_openmp_compatible(nb_threads)
self.write_static_arrays(directory)
self.find_synapses()
# Not sure what the best place is to call Network.after_run -- at the
# moment the only important thing it does is to clear the objects stored
# in magic_network. If this is not done, this might lead to problems
# for repeated runs of standalone (e.g. in the test suite).
for net in self.networks:
net.after_run()
# Check that all names are globally unique
names = [obj.name for net in self.networks for obj in net.objects]
non_unique_names = [name for name, count in Counter(names).items() if count > 1]
if len(non_unique_names):
formatted_names = ", ".join("'%s'" % name for name in non_unique_names)
raise ValueError(
"All objects need to have unique names in "
"standalone mode, the following name(s) were used "
"more than once: %s" % formatted_names
)
self.generate_objects_source(
self.writer,
self.arange_arrays,
self.net_synapses,
self.static_array_specs,
self.networks,
)
self.generate_main_source(self.writer)
self.generate_codeobj_source(self.writer)
self.generate_network_source(self.writer, compiler)
self.generate_synapses_classes_source(self.writer)
self.generate_run_source(self.writer)
self.copy_source_files(self.writer, directory)
self.writer.source_files.extend(additional_source_files)
self.generate_makefile(
self.writer,
compiler,
compiler_flags=" ".join(compiler_flags),
linker_flags=" ".join(linker_flags),
nb_threads=nb_threads,
debug=debug,
)
if compile:
self.compile_source(directory, compiler, debug, clean)
if run:
self.run(directory, with_output, run_args)
|
https://github.com/brian-team/brian2/issues/1189
|
ERROR Brian 2 encountered an unexpected error. If you think this is bug in Brian 2, please report this issue either to the mailing list at <http://groups.google.com/group/brian-development/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_debug_1uynejn5.log Additionally, you can also include a copy of the script that was run, available at: /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_script_m_84dmg4.py You can also include a copy of the redirected std stream outputs, available at /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_stdout_d2yd1ugv.log and /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_stderr_xkxqltw0.log Thanks! [brian2]
Traceback (most recent call last):
File "/Users/fpbatta/src/assembly_sequences/scripts/run_simulation_simple.py", line 69, in <module>
nn1 = network_sim()
File "/Users/fpbatta/src/assembly_sequences/scripts/run_simulation_simple.py", line 59, in network_sim
bb.get_device().build(directory='PETH_standalone', compile=True, run=True, debug=False)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/device.py", line 1265, in build
self.generate_objects_source(self.writer, self.arange_arrays,
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/device.py", line 633, in generate_objects_source
arr_tmp = self.code_object_class().templater.objects(
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/codegen/templates.py", line 210, in __call__
return MultiTemplate(module)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/codegen/templates.py", line 226, in __init__
s = autoindent_postfilter(str(f()))
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 675, in __call__
return self._invoke(arguments, autoescape)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 679, in _invoke
rv = self._func(*arguments)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/templates/objects.cpp", line 122, in macro
if(f{{name}}.is_open())
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 747, in _fail_with_undefined_error
raise self._undefined_exception(self._undefined_message)
jinja2.exceptions.UndefinedError: dict object has no element <DynamicArrayVariable(dimensions=Dimension(), dtype=int32, scalar=False, constant=True, read_only=True)>
|
jinja2.exceptions.UndefinedError
|
def network_run(
self,
net,
duration,
report=None,
report_period=10 * second,
namespace=None,
profile=False,
level=0,
**kwds,
):
self.networks.add(net)
if kwds:
logger.warn(
("Unsupported keyword argument(s) provided for run: %s")
% ", ".join(kwds.keys())
)
# We store this as an instance variable for later access by the
# `code_object` method
self.enable_profiling = profile
all_objects = net.sorted_objects
net._clocks = {obj.clock for obj in all_objects}
t_end = net.t + duration
for clock in net._clocks:
clock.set_interval(net.t, t_end)
# Get the local namespace
if namespace is None:
namespace = get_local_namespace(level=level + 2)
net.before_run(namespace)
self.clocks.update(net._clocks)
net.t_ = float(t_end)
# TODO: remove this horrible hack
for clock in self.clocks:
if clock.name == "clock":
clock._name = "_clock"
# Extract all the CodeObjects
# Note that since we ran the Network object, these CodeObjects will be sorted into the right
# running order, assuming that there is only one clock
code_objects = []
for obj in all_objects:
if obj.active:
for codeobj in obj._code_objects:
code_objects.append((obj.clock, codeobj))
# Code for a progress reporting function
standard_code = """
std::string _format_time(float time_in_s)
{
float divisors[] = {24*60*60, 60*60, 60, 1};
char letters[] = {'d', 'h', 'm', 's'};
float remaining = time_in_s;
std::string text = "";
int time_to_represent;
for (int i =0; i < sizeof(divisors)/sizeof(float); i++)
{
time_to_represent = int(remaining / divisors[i]);
remaining -= time_to_represent * divisors[i];
if (time_to_represent > 0 || text.length())
{
if(text.length() > 0)
{
text += " ";
}
text += (std::to_string(time_to_represent)+letters[i]);
}
}
//less than one second
if(text.length() == 0)
{
text = "< 1s";
}
return text;
}
void report_progress(const double elapsed, const double completed, const double start, const double duration)
{
if (completed == 0.0)
{
%STREAMNAME% << "Starting simulation at t=" << start << " s for duration " << duration << " s";
} else
{
%STREAMNAME% << completed*duration << " s (" << (int)(completed*100.) << "%) simulated in " << _format_time(elapsed);
if (completed < 1.0)
{
const int remaining = (int)((1-completed)/completed*elapsed+0.5);
%STREAMNAME% << ", estimated " << _format_time(remaining) << " remaining.";
}
}
%STREAMNAME% << std::endl << std::flush;
}
"""
if report is None:
report_func = ""
elif report == "text" or report == "stdout":
report_func = standard_code.replace("%STREAMNAME%", "std::cout")
elif report == "stderr":
report_func = standard_code.replace("%STREAMNAME%", "std::cerr")
elif isinstance(report, str):
report_func = """
void report_progress(const double elapsed, const double completed, const double start, const double duration)
{
%REPORT%
}
""".replace("%REPORT%", report)
else:
raise TypeError(
(
'report argument has to be either "text", '
'"stdout", "stderr", or the code for a report '
"function"
)
)
if report_func != "":
if self.report_func != "" and report_func != self.report_func:
raise NotImplementedError(
"The C++ standalone device does not "
"support multiple report functions, "
"each run has to use the same (or "
"none)."
)
self.report_func = report_func
if report is not None:
report_call = "report_progress"
else:
report_call = "NULL"
# Generate the updaters
run_lines = ["{net.name}.clear();".format(net=net)]
all_clocks = set()
for clock, codeobj in code_objects:
run_lines.append(
"{net.name}.add(&{clock.name}, _run_{codeobj.name});".format(
clock=clock, net=net, codeobj=codeobj
)
)
all_clocks.add(clock)
# Under some rare circumstances (e.g. a NeuronGroup only defining a
# subexpression that is used by other groups (via linking, or recorded
# by a StateMonitor) *and* not calculating anything itself *and* using a
# different clock than all other objects) a clock that is not used by
# any code object should nevertheless advance during the run. We include
# such clocks without a code function in the network.
for clock in net._clocks:
if clock not in all_clocks:
run_lines.append(
"{net.name}.add(&{clock.name}, NULL);".format(clock=clock, net=net)
)
run_lines.append(
"{net.name}.run({duration!r}, {report_call}, {report_period!r});".format(
net=net,
duration=float(duration),
report_call=report_call,
report_period=float(report_period),
)
)
self.main_queue.append(("run_network", (net, run_lines)))
# Manually set the cache for the clocks, simulation scripts might
# want to access the time (which has been set in code and is therefore
# not accessible by the normal means until the code has been built and
# run)
for clock in net._clocks:
self.array_cache[clock.variables["timestep"]] = np.array([clock._i_end])
self.array_cache[clock.variables["t"]] = np.array([clock._i_end * clock.dt_])
if self.build_on_run:
if self.has_been_run:
raise RuntimeError(
"The network has already been built and run "
"before. Use set_device with "
"build_on_run=False and an explicit "
"device.build call to use multiple run "
"statements with this device."
)
self.build(direct_call=False, **self.build_options)
|
def network_run(
self,
net,
duration,
report=None,
report_period=10 * second,
namespace=None,
profile=False,
level=0,
**kwds,
):
if kwds:
logger.warn(
("Unsupported keyword argument(s) provided for run: %s")
% ", ".join(kwds.keys())
)
# We store this as an instance variable for later access by the
# `code_object` method
self.enable_profiling = profile
all_objects = net.sorted_objects
net._clocks = {obj.clock for obj in all_objects}
t_end = net.t + duration
for clock in net._clocks:
clock.set_interval(net.t, t_end)
# Get the local namespace
if namespace is None:
namespace = get_local_namespace(level=level + 2)
net.before_run(namespace)
self.clocks.update(net._clocks)
net.t_ = float(t_end)
# TODO: remove this horrible hack
for clock in self.clocks:
if clock.name == "clock":
clock._name = "_clock"
# Extract all the CodeObjects
# Note that since we ran the Network object, these CodeObjects will be sorted into the right
# running order, assuming that there is only one clock
code_objects = []
for obj in all_objects:
if obj.active:
for codeobj in obj._code_objects:
code_objects.append((obj.clock, codeobj))
# Code for a progress reporting function
standard_code = """
std::string _format_time(float time_in_s)
{
float divisors[] = {24*60*60, 60*60, 60, 1};
char letters[] = {'d', 'h', 'm', 's'};
float remaining = time_in_s;
std::string text = "";
int time_to_represent;
for (int i =0; i < sizeof(divisors)/sizeof(float); i++)
{
time_to_represent = int(remaining / divisors[i]);
remaining -= time_to_represent * divisors[i];
if (time_to_represent > 0 || text.length())
{
if(text.length() > 0)
{
text += " ";
}
text += (std::to_string(time_to_represent)+letters[i]);
}
}
//less than one second
if(text.length() == 0)
{
text = "< 1s";
}
return text;
}
void report_progress(const double elapsed, const double completed, const double start, const double duration)
{
if (completed == 0.0)
{
%STREAMNAME% << "Starting simulation at t=" << start << " s for duration " << duration << " s";
} else
{
%STREAMNAME% << completed*duration << " s (" << (int)(completed*100.) << "%) simulated in " << _format_time(elapsed);
if (completed < 1.0)
{
const int remaining = (int)((1-completed)/completed*elapsed+0.5);
%STREAMNAME% << ", estimated " << _format_time(remaining) << " remaining.";
}
}
%STREAMNAME% << std::endl << std::flush;
}
"""
if report is None:
report_func = ""
elif report == "text" or report == "stdout":
report_func = standard_code.replace("%STREAMNAME%", "std::cout")
elif report == "stderr":
report_func = standard_code.replace("%STREAMNAME%", "std::cerr")
elif isinstance(report, str):
report_func = """
void report_progress(const double elapsed, const double completed, const double start, const double duration)
{
%REPORT%
}
""".replace("%REPORT%", report)
else:
raise TypeError(
(
'report argument has to be either "text", '
'"stdout", "stderr", or the code for a report '
"function"
)
)
if report_func != "":
if self.report_func != "" and report_func != self.report_func:
raise NotImplementedError(
"The C++ standalone device does not "
"support multiple report functions, "
"each run has to use the same (or "
"none)."
)
self.report_func = report_func
if report is not None:
report_call = "report_progress"
else:
report_call = "NULL"
# Generate the updaters
run_lines = ["{net.name}.clear();".format(net=net)]
all_clocks = set()
for clock, codeobj in code_objects:
run_lines.append(
"{net.name}.add(&{clock.name}, _run_{codeobj.name});".format(
clock=clock, net=net, codeobj=codeobj
)
)
all_clocks.add(clock)
# Under some rare circumstances (e.g. a NeuronGroup only defining a
# subexpression that is used by other groups (via linking, or recorded
# by a StateMonitor) *and* not calculating anything itself *and* using a
# different clock than all other objects) a clock that is not used by
# any code object should nevertheless advance during the run. We include
# such clocks without a code function in the network.
for clock in net._clocks:
if clock not in all_clocks:
run_lines.append(
"{net.name}.add(&{clock.name}, NULL);".format(clock=clock, net=net)
)
run_lines.append(
"{net.name}.run({duration!r}, {report_call}, {report_period!r});".format(
net=net,
duration=float(duration),
report_call=report_call,
report_period=float(report_period),
)
)
self.main_queue.append(("run_network", (net, run_lines)))
# Manually set the cache for the clocks, simulation scripts might
# want to access the time (which has been set in code and is therefore
# not accessible by the normal means until the code has been built and
# run)
for clock in net._clocks:
self.array_cache[clock.variables["timestep"]] = np.array([clock._i_end])
self.array_cache[clock.variables["t"]] = np.array([clock._i_end * clock.dt_])
if self.build_on_run:
if self.has_been_run:
raise RuntimeError(
"The network has already been built and run "
"before. Use set_device with "
"build_on_run=False and an explicit "
"device.build call to use multiple run "
"statements with this device."
)
self.build(direct_call=False, **self.build_options)
|
https://github.com/brian-team/brian2/issues/1189
|
ERROR Brian 2 encountered an unexpected error. If you think this is bug in Brian 2, please report this issue either to the mailing list at <http://groups.google.com/group/brian-development/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_debug_1uynejn5.log Additionally, you can also include a copy of the script that was run, available at: /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_script_m_84dmg4.py You can also include a copy of the redirected std stream outputs, available at /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_stdout_d2yd1ugv.log and /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_stderr_xkxqltw0.log Thanks! [brian2]
Traceback (most recent call last):
File "/Users/fpbatta/src/assembly_sequences/scripts/run_simulation_simple.py", line 69, in <module>
nn1 = network_sim()
File "/Users/fpbatta/src/assembly_sequences/scripts/run_simulation_simple.py", line 59, in network_sim
bb.get_device().build(directory='PETH_standalone', compile=True, run=True, debug=False)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/device.py", line 1265, in build
self.generate_objects_source(self.writer, self.arange_arrays,
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/device.py", line 633, in generate_objects_source
arr_tmp = self.code_object_class().templater.objects(
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/codegen/templates.py", line 210, in __call__
return MultiTemplate(module)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/codegen/templates.py", line 226, in __init__
s = autoindent_postfilter(str(f()))
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 675, in __call__
return self._invoke(arguments, autoescape)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 679, in _invoke
rv = self._func(*arguments)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/templates/objects.cpp", line 122, in macro
if(f{{name}}.is_open())
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 747, in _fail_with_undefined_error
raise self._undefined_exception(self._undefined_message)
jinja2.exceptions.UndefinedError: dict object has no element <DynamicArrayVariable(dimensions=Dimension(), dtype=int32, scalar=False, constant=True, read_only=True)>
|
jinja2.exceptions.UndefinedError
|
def network_run(
self,
net,
duration,
report=None,
report_period=10 * second,
namespace=None,
profile=False,
level=0,
**kwds,
):
self.networks.add(net)
if kwds:
logger.warn(
("Unsupported keyword argument(s) provided for run: %s")
% ", ".join(kwds.keys())
)
# We store this as an instance variable for later access by the
# `code_object` method
self.enable_profiling = profile
all_objects = net.sorted_objects
net._clocks = {obj.clock for obj in all_objects}
t_end = net.t + duration
for clock in net._clocks:
clock.set_interval(net.t, t_end)
# Get the local namespace
if namespace is None:
namespace = get_local_namespace(level=level + 2)
net.before_run(namespace)
self.clocks.update(net._clocks)
net.t_ = float(t_end)
# TODO: remove this horrible hack
for clock in self.clocks:
if clock.name == "clock":
clock._name = "_clock"
# Extract all the CodeObjects
# Note that since we ran the Network object, these CodeObjects will be sorted into the right
# running order, assuming that there is only one clock
code_objects = []
for obj in all_objects:
if obj.active:
for codeobj in obj._code_objects:
code_objects.append((obj.clock, codeobj))
# Code for a progress reporting function
standard_code = """
void report_progress(const double elapsed, const double completed, const double start, const double duration)
{
if (completed == 0.0)
{
%STREAMNAME% << "Starting simulation at t=" << start << " s for duration " << duration << " s";
} else
{
%STREAMNAME% << completed*duration << " s (" << (int)(completed*100.) << "%) simulated in " << elapsed << " s";
if (completed < 1.0)
{
const int remaining = (int)((1-completed)/completed*elapsed+0.5);
%STREAMNAME% << ", estimated " << remaining << " s remaining.";
}
}
%STREAMNAME% << std::endl << std::flush;
}
"""
if report is None:
report_func = ""
elif report == "text" or report == "stdout":
report_func = standard_code.replace("%STREAMNAME%", "std::cout")
elif report == "stderr":
report_func = standard_code.replace("%STREAMNAME%", "std::cerr")
elif isinstance(report, str):
report_func = """
void report_progress(const double elapsed, const double completed, const double start, const double duration)
{
%REPORT%
}
""".replace("%REPORT%", report)
else:
raise TypeError(
(
'report argument has to be either "text", '
'"stdout", "stderr", or the code for a report '
"function"
)
)
if report_func != "":
if self.report_func != "" and report_func != self.report_func:
raise NotImplementedError(
"The C++ standalone device does not "
"support multiple report functions, "
"each run has to use the same (or "
"none)."
)
self.report_func = report_func
if report is not None:
report_call = "report_progress"
else:
report_call = "NULL"
# Generate the updaters
run_lines = ["{net.name}.clear();".format(net=net)]
all_clocks = set()
for clock, codeobj in code_objects:
run_lines.append(
"{net.name}.add(&{clock.name}, _run_{codeobj.name});".format(
clock=clock, net=net, codeobj=codeobj
)
)
all_clocks.add(clock)
# Under some rare circumstances (e.g. a NeuronGroup only defining a
# subexpression that is used by other groups (via linking, or recorded
# by a StateMonitor) *and* not calculating anything itself *and* using a
# different clock than all other objects) a clock that is not used by
# any code object should nevertheless advance during the run. We include
# such clocks without a code function in the network.
for clock in net._clocks:
if clock not in all_clocks:
run_lines.append(
"{net.name}.add(&{clock.name}, NULL);".format(clock=clock, net=net)
)
run_lines.append(
"{net.name}.run({duration!r}, {report_call}, {report_period!r});".format(
net=net,
duration=float(duration),
report_call=report_call,
report_period=float(report_period),
)
)
self.main_queue.append(("run_network", (net, run_lines)))
# Manually set the cache for the clocks, simulation scripts might
# want to access the time (which has been set in code and is therefore
# not accessible by the normal means until the code has been built and
# run)
for clock in net._clocks:
self.array_cache[clock.variables["timestep"]] = np.array([clock._i_end])
self.array_cache[clock.variables["t"]] = np.array([clock._i_end * clock.dt_])
if self.build_on_run:
if self.has_been_run:
raise RuntimeError(
"The network has already been built and run "
"before. Use set_device with "
"build_on_run=False and an explicit "
"device.build call to use multiple run "
"statements with this device."
)
self.build(direct_call=False, **self.build_options)
|
def network_run(
self,
net,
duration,
report=None,
report_period=10 * second,
namespace=None,
profile=False,
level=0,
**kwds,
):
if kwds:
logger.warn(
("Unsupported keyword argument(s) provided for run: %s")
% ", ".join(kwds.keys())
)
# We store this as an instance variable for later access by the
# `code_object` method
self.enable_profiling = profile
all_objects = net.sorted_objects
net._clocks = {obj.clock for obj in all_objects}
t_end = net.t + duration
for clock in net._clocks:
clock.set_interval(net.t, t_end)
# Get the local namespace
if namespace is None:
namespace = get_local_namespace(level=level + 2)
net.before_run(namespace)
self.clocks.update(net._clocks)
net.t_ = float(t_end)
# TODO: remove this horrible hack
for clock in self.clocks:
if clock.name == "clock":
clock._name = "_clock"
# Extract all the CodeObjects
# Note that since we ran the Network object, these CodeObjects will be sorted into the right
# running order, assuming that there is only one clock
code_objects = []
for obj in all_objects:
if obj.active:
for codeobj in obj._code_objects:
code_objects.append((obj.clock, codeobj))
# Code for a progress reporting function
standard_code = """
void report_progress(const double elapsed, const double completed, const double start, const double duration)
{
if (completed == 0.0)
{
%STREAMNAME% << "Starting simulation at t=" << start << " s for duration " << duration << " s";
} else
{
%STREAMNAME% << completed*duration << " s (" << (int)(completed*100.) << "%) simulated in " << elapsed << " s";
if (completed < 1.0)
{
const int remaining = (int)((1-completed)/completed*elapsed+0.5);
%STREAMNAME% << ", estimated " << remaining << " s remaining.";
}
}
%STREAMNAME% << std::endl << std::flush;
}
"""
if report is None:
report_func = ""
elif report == "text" or report == "stdout":
report_func = standard_code.replace("%STREAMNAME%", "std::cout")
elif report == "stderr":
report_func = standard_code.replace("%STREAMNAME%", "std::cerr")
elif isinstance(report, str):
report_func = """
void report_progress(const double elapsed, const double completed, const double start, const double duration)
{
%REPORT%
}
""".replace("%REPORT%", report)
else:
raise TypeError(
(
'report argument has to be either "text", '
'"stdout", "stderr", or the code for a report '
"function"
)
)
if report_func != "":
if self.report_func != "" and report_func != self.report_func:
raise NotImplementedError(
"The C++ standalone device does not "
"support multiple report functions, "
"each run has to use the same (or "
"none)."
)
self.report_func = report_func
if report is not None:
report_call = "report_progress"
else:
report_call = "NULL"
# Generate the updaters
run_lines = ["{net.name}.clear();".format(net=net)]
all_clocks = set()
for clock, codeobj in code_objects:
run_lines.append(
"{net.name}.add(&{clock.name}, _run_{codeobj.name});".format(
clock=clock, net=net, codeobj=codeobj
)
)
all_clocks.add(clock)
# Under some rare circumstances (e.g. a NeuronGroup only defining a
# subexpression that is used by other groups (via linking, or recorded
# by a StateMonitor) *and* not calculating anything itself *and* using a
# different clock than all other objects) a clock that is not used by
# any code object should nevertheless advance during the run. We include
# such clocks without a code function in the network.
for clock in net._clocks:
if clock not in all_clocks:
run_lines.append(
"{net.name}.add(&{clock.name}, NULL);".format(clock=clock, net=net)
)
run_lines.append(
"{net.name}.run({duration!r}, {report_call}, {report_period!r});".format(
net=net,
duration=float(duration),
report_call=report_call,
report_period=float(report_period),
)
)
self.main_queue.append(("run_network", (net, run_lines)))
# Manually set the cache for the clocks, simulation scripts might
# want to access the time (which has been set in code and is therefore
# not accessible by the normal means until the code has been built and
# run)
for clock in net._clocks:
self.array_cache[clock.variables["timestep"]] = np.array([clock._i_end])
self.array_cache[clock.variables["t"]] = np.array([clock._i_end * clock.dt_])
if self.build_on_run:
if self.has_been_run:
raise RuntimeError(
"The network has already been built and run "
"before. Use set_device with "
"build_on_run=False and an explicit "
"device.build call to use multiple run "
"statements with this device."
)
self.build(direct_call=False, **self.build_options)
|
https://github.com/brian-team/brian2/issues/1189
|
ERROR Brian 2 encountered an unexpected error. If you think this is bug in Brian 2, please report this issue either to the mailing list at <http://groups.google.com/group/brian-development/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_debug_1uynejn5.log Additionally, you can also include a copy of the script that was run, available at: /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_script_m_84dmg4.py You can also include a copy of the redirected std stream outputs, available at /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_stdout_d2yd1ugv.log and /var/folders/_n/ml20bf7n0_g3sz165pd3nrjm0000gn/T/brian_stderr_xkxqltw0.log Thanks! [brian2]
Traceback (most recent call last):
File "/Users/fpbatta/src/assembly_sequences/scripts/run_simulation_simple.py", line 69, in <module>
nn1 = network_sim()
File "/Users/fpbatta/src/assembly_sequences/scripts/run_simulation_simple.py", line 59, in network_sim
bb.get_device().build(directory='PETH_standalone', compile=True, run=True, debug=False)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/device.py", line 1265, in build
self.generate_objects_source(self.writer, self.arange_arrays,
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/device.py", line 633, in generate_objects_source
arr_tmp = self.code_object_class().templater.objects(
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/codegen/templates.py", line 210, in __call__
return MultiTemplate(module)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/codegen/templates.py", line 226, in __init__
s = autoindent_postfilter(str(f()))
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 675, in __call__
return self._invoke(arguments, autoescape)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 679, in _invoke
rv = self._func(*arguments)
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/brian2/devices/cpp_standalone/templates/objects.cpp", line 122, in macro
if(f{{name}}.is_open())
File "/Users/fpbatta/.conda/envs/brian23/lib/python3.8/site-packages/jinja2/runtime.py", line 747, in _fail_with_undefined_error
raise self._undefined_exception(self._undefined_message)
jinja2.exceptions.UndefinedError: dict object has no element <DynamicArrayVariable(dimensions=Dimension(), dtype=int32, scalar=False, constant=True, read_only=True)>
|
jinja2.exceptions.UndefinedError
|
def brian_object_exception(message, brianobj, original_exception):
"""
Returns a `BrianObjectException` derived from the original exception.
Creates a new class derived from the class of the original exception
and `BrianObjectException`. This allows exception handling code to
respond both to the original exception class and `BrianObjectException`.
See `BrianObjectException` for arguments and notes.
"""
DerivedBrianObjectException = type(
"BrianObjectException", (BrianObjectException, original_exception.__class__), {}
)
new_exception = DerivedBrianObjectException(message, brianobj, original_exception)
# Copy over all exception attributes
for attribute in dir(original_exception):
if attribute.startswith("_"):
continue
setattr(new_exception, attribute, getattr(original_exception, attribute))
return new_exception
|
def brian_object_exception(message, brianobj, original_exception):
"""
Returns a `BrianObjectException` derived from the original exception.
Creates a new class derived from the class of the original exception
and `BrianObjectException`. This allows exception handling code to
respond both to the original exception class and `BrianObjectException`.
See `BrianObjectException` for arguments and notes.
"""
DerivedBrianObjectException = type(
"BrianObjectException", (BrianObjectException, original_exception.__class__), {}
)
return DerivedBrianObjectException(message, brianobj, original_exception)
|
https://github.com/brian-team/brian2/issues/964
|
Traceback (most recent call last):
File "err_test.py", line 5, in <module>
run(0*ms)
File "/home/marcel/programming/brian2/brian2/units/fundamentalunits.py", line 2360, in new_f
result = f(*args, **kwds)
File "/home/marcel/programming/brian2/brian2/core/magic.py", line 371, in run
namespace=namespace, profile=profile, level=2+level)
File "/home/marcel/programming/brian2/brian2/core/magic.py", line 231, in run
namespace=namespace, profile=profile, level=level+1)
File "/home/marcel/programming/brian2/brian2/core/base.py", line 278, in device_override_decorated_function
return func(*args, **kwds)
File "/home/marcel/programming/brian2/brian2/units/fundamentalunits.py", line 2360, in new_f
result = f(*args, **kwds)
File "/home/marcel/programming/brian2/brian2/core/network.py", line 951, in run
self.before_run(namespace)
File "/home/marcel/programming/brian2/brian2/core/base.py", line 278, in device_override_decorated_function
return func(*args, **kwds)
File "/home/marcel/programming/brian2/brian2/core/network.py", line 843, in before_run
raise brian_object_exception("An error occurred when preparing an object.", obj, ex)
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "/home/marcel/programming/brian2/brian2/core/network.py", line 841, in before_run
obj.before_run(run_namespace)
File "/home/marcel/programming/brian2/brian2/groups/group.py", line 1093, in before_run
self.update_abstract_code(run_namespace=run_namespace)
File "/home/marcel/programming/brian2/brian2/groups/neurongroup.py", line 267, in update_abstract_code
if not is_boolean_expression(code, variables):
File "/home/marcel/programming/brian2/brian2/parsing/expressions.py", line 64, in is_boolean_expression
mod = ast.parse(expr, mode='eval')
File "/home/marcel/anaconda2/envs/brian2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 1
`False
^
SyntaxError: unexpected EOF while parsing
Error encountered with object named "neurongroup_thresholder".
Object was created here (most recent call only, full details in debug log):
File "err_test.py", line 3, in <module>
g = NeuronGroup(1, '', threshold='`False')
An error occurred when preparing an object. File "<unknown>", line 1
`False
^
SyntaxError: unexpected EOF while parsing
(See above for original error message and traceback.)
|
SyntaxError
|
def conditional_write(
self, line, stmt, variables, conditional_write_vars, created_vars
):
if stmt.var in conditional_write_vars:
subs = {}
index = conditional_write_vars[stmt.var]
# we replace all var with var[index], but actually we use this repl_string first because
# we don't want to end up with lines like x[not_refractory[not_refractory]] when
# multiple substitution passes are invoked
repl_string = (
"#$(@#&$@$*U#@)$@(#" # this string shouldn't occur anywhere I hope! :)
)
for varname, var in variables.items():
if isinstance(var, ArrayVariable) and not var.scalar:
subs[varname] = varname + "[" + repl_string + "]"
# all newly created vars are arrays and will need indexing
for varname in created_vars:
subs[varname] = varname + "[" + repl_string + "]"
# Also index _vectorisation_idx so that e.g. rand() works correctly
subs["_vectorisation_idx"] = "_vectorisation_idx" + "[" + repl_string + "]"
line = word_substitute(line, subs)
line = line.replace(repl_string, index)
return line
|
def conditional_write(
self, line, stmt, variables, conditional_write_vars, created_vars
):
if stmt.var in conditional_write_vars:
subs = {}
index = conditional_write_vars[stmt.var]
# we replace all var with var[index], but actually we use this repl_string first because
# we don't want to end up with lines like x[not_refractory[not_refractory]] when
# multiple substitution passes are invoked
repl_string = (
"#$(@#&$@$*U#@)$@(#" # this string shouldn't occur anywhere I hope! :)
)
for varname, var in variables.items():
if isinstance(var, ArrayVariable) and not var.scalar:
subs[varname] = varname + "[" + repl_string + "]"
# all newly created vars are arrays and will need indexing
for varname in created_vars:
subs[varname] = varname + "[" + repl_string + "]"
line = word_substitute(line, subs)
line = line.replace(repl_string, index)
return line
|
https://github.com/brian-team/brian2/issues/761
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "E:\Dan\programming\brian2\brian2\codegen\runtime\numpy_rt\numpy_rt.py", line 122, in run
exec self.compiled_code in self.namespace
File "(string)", line 13, in <module>
ValueError: operands could not be broadcast together with shapes (99,) (100,) (99,)
Error encountered with object named "neurongroup_1".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-2-ff5506ac93b4>", line 9, in <module>
G = NeuronGroup(100, eqs, reset='v=0', threshold='v>1', refractory=1*ms)
An exception occured during the execution of code object poissoninput_1_codeobject.
The error was raised in the following line:
v[not_refractory] += 0.1 * poissoninput_binomial_1(_vectorisation_idx)
ValueError: operands could not be broadcast together with shapes (99,) (100,) (99,)
(See above for original error message and traceback.)
|
ValueError
|
def randn_func(vectorisation_idx):
try:
N = len(vectorisation_idx)
return np.random.randn(N)
except TypeError:
# scalar value
return np.random.randn()
|
def randn_func(vectorisation_idx):
try:
N = len(vectorisation_idx)
except TypeError:
N = int(vectorisation_idx)
numbers = np.random.randn(N)
if N == 1:
return numbers[0]
else:
return numbers
|
https://github.com/brian-team/brian2/issues/761
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "E:\Dan\programming\brian2\brian2\codegen\runtime\numpy_rt\numpy_rt.py", line 122, in run
exec self.compiled_code in self.namespace
File "(string)", line 13, in <module>
ValueError: operands could not be broadcast together with shapes (99,) (100,) (99,)
Error encountered with object named "neurongroup_1".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-2-ff5506ac93b4>", line 9, in <module>
G = NeuronGroup(100, eqs, reset='v=0', threshold='v>1', refractory=1*ms)
An exception occured during the execution of code object poissoninput_1_codeobject.
The error was raised in the following line:
v[not_refractory] += 0.1 * poissoninput_binomial_1(_vectorisation_idx)
ValueError: operands could not be broadcast together with shapes (99,) (100,) (99,)
(See above for original error message and traceback.)
|
ValueError
|
def rand_func(vectorisation_idx):
try:
N = len(vectorisation_idx)
return np.random.rand(N)
except TypeError:
# scalar value
return np.random.rand()
|
def rand_func(vectorisation_idx):
try:
N = len(vectorisation_idx)
except TypeError:
N = int(vectorisation_idx)
numbers = np.random.rand(N)
if N == 1:
return numbers[0]
else:
return numbers
|
https://github.com/brian-team/brian2/issues/761
|
BrianObjectException: Original error and traceback:
Traceback (most recent call last):
File "E:\Dan\programming\brian2\brian2\codegen\runtime\numpy_rt\numpy_rt.py", line 122, in run
exec self.compiled_code in self.namespace
File "(string)", line 13, in <module>
ValueError: operands could not be broadcast together with shapes (99,) (100,) (99,)
Error encountered with object named "neurongroup_1".
Object was created here (most recent call only, full details in debug log):
File "<ipython-input-2-ff5506ac93b4>", line 9, in <module>
G = NeuronGroup(100, eqs, reset='v=0', threshold='v>1', refractory=1*ms)
An exception occured during the execution of code object poissoninput_1_codeobject.
The error was raised in the following line:
v[not_refractory] += 0.1 * poissoninput_binomial_1(_vectorisation_idx)
ValueError: operands could not be broadcast together with shapes (99,) (100,) (99,)
(See above for original error message and traceback.)
|
ValueError
|
def restore(self, name="default", filename=None):
"""
restore(name='default', filename=None)
Retore the state of the network and all included objects.
Parameters
----------
name : str, optional
The name of the snapshot to restore, if not specified uses
``'default'``.
filename : str, optional
The name of the file from where the state should be restored. If
not specified, it is expected that the state exist in memory
(i.e. `Network.store` was previously called without the ``filename``
argument).
"""
if filename is None:
state = self._stored_state[name]
else:
with open(filename, "rb") as f:
state = pickle.load(f)[name]
self.t_ = state["0_t"]
clocks = set([obj.clock for obj in self.objects])
restored_objects = set()
for obj in self.objects:
if obj.name in state:
obj._restore_from_full_state(state[obj.name])
restored_objects.add(obj.name)
elif hasattr(obj, "_restore_from_full_state"):
raise KeyError(
(
"Stored state does not have a stored state for "
'"%s". Note that the names of all objects have '
"to be identical to the names when they were "
"stored."
)
% obj.name
)
for clock in clocks:
clock._restore_from_full_state(state[clock.name])
clock_names = {c.name for c in clocks}
unnused = set(state.keys()) - restored_objects - clock_names - {"0_t"}
if len(unnused):
raise KeyError(
"The stored state contains the state of the "
"following objects which were not present in the "
"network: %s. Note that the names of all objects "
"have to be identical to the names when they were "
"stored." % (", ".join(unnused))
)
|
def restore(self, name="default", filename=None):
"""
restore(name='default', filename=None)
Retore the state of the network and all included objects.
Parameters
----------
name : str, optional
The name of the snapshot to restore, if not specified uses
``'default'``.
filename : str, optional
The name of the file from where the state should be restored. If
not specified, it is expected that the state exist in memory
(i.e. `Network.store` was previously called without the ``filename``
argument).
"""
if filename is None:
state = self._stored_state[name]
else:
with open(filename, "rb") as f:
state = pickle.load(f)[name]
self.t_ = state.pop("0_t")
clocks = set([obj.clock for obj in self.objects])
restored_objects = set()
for obj in self.objects:
if obj.name in state:
obj._restore_from_full_state(state[obj.name])
restored_objects.add(obj.name)
elif hasattr(obj, "_restore_from_full_state"):
raise KeyError(
(
"Stored state does not have a stored state for "
'"%s". Note that the names of all objects have '
"to be identical to the names when they were "
"stored."
)
% obj.name
)
for clock in clocks:
clock._restore_from_full_state(state[clock.name])
clock_names = {c.name for c in clocks}
unnused = set(state.keys()) - restored_objects - clock_names
if len(unnused):
raise KeyError(
"The stored state contains the state of the "
"following objects which were not present in the "
"network: %s. Note that the names of all objects "
"have to be identical to the names when they were "
"stored." % (", ".join(unnused))
)
|
https://github.com/brian-team/brian2/issues/681
|
In [1]: from brian2 import *
In [2]: G = NeuronGroup(1, 'v: 1')
In [3]: store()
In [4]: restore()
In [5]: restore()
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-5-ad7bb0bcaaad> in <module>()
----> 1 restore()
/home/marcel/programming/brian2/brian2/core/magic.pyc in restore(name, filename)
411 Network.restore
412 '''
--> 413 magic_network.restore(name=name, filename=filename, level=1)
414
415
/home/marcel/programming/brian2/brian2/core/magic.pyc in restore(self, name, filename, level)
244 '''
245 self._update_magic_objects(level=level+1)
--> 246 super(MagicNetwork, self).restore(name=name, filename=filename)
247 self.objects[:] = []
248
/home/marcel/programming/brian2/brian2/core/base.pyc in device_override_decorated_function(*args, **kwds)
276 return getattr(curdev, name)(*args, **kwds)
277 else:
--> 278 return func(*args, **kwds)
279
280 device_override_decorated_function.__doc__ = func.__doc__
/home/marcel/programming/brian2/brian2/core/network.pyc in restore(self, name, filename)
431 with open(filename, 'rb') as f:
432 state = pickle.load(f)[name]
--> 433 self.t_ = state.pop('0_t')
434 clocks = set([obj.clock for obj in self.objects])
435 restored_objects = set()
KeyError: '0_t'
|
KeyError
|
def push(self, sources):
"""
Push spikes to the queue.
Parameters
----------
sources : ndarray of int
The indices of the neurons that spiked.
"""
if len(sources) and len(self._delays):
start = self._source_start
stop = self._source_end
if start > 0:
start_idx = bisect.bisect_left(sources, start)
else:
start_idx = 0
if stop <= sources[-1]:
stop_idx = bisect.bisect_left(sources, stop, lo=start_idx)
else:
stop_idx = len(self._neurons_to_synapses)
sources = sources[start_idx:stop_idx]
if len(sources) == 0:
return
synapse_indices = self._neurons_to_synapses
indices = np.concatenate(
[synapse_indices[source - start] for source in sources]
).astype(np.int32)
if self._homogeneous: # homogeneous delays
self._insert_homogeneous(self._delays[0], indices)
elif self._offsets is None: # vectorise over synaptic events
# there are no precomputed offsets, this is the case
# (in particular) when there are dynamic delays
self._insert(self._delays[indices], indices)
else: # offsets are precomputed
self._insert(self._delays[indices], indices, self._offsets[indices])
|
def push(self, sources):
"""
Push spikes to the queue.
Parameters
----------
sources : ndarray of int
The indices of the neurons that spiked.
"""
if len(sources):
start = self._source_start
stop = self._source_end
if start > 0:
start_idx = bisect.bisect_left(sources, start)
else:
start_idx = 0
if stop <= sources[-1]:
stop_idx = bisect.bisect_left(sources, stop, lo=start_idx)
else:
stop_idx = len(self._neurons_to_synapses)
sources = sources[start_idx:stop_idx]
if len(sources) == 0:
return
synapse_indices = self._neurons_to_synapses
indices = np.concatenate(
[synapse_indices[source - start] for source in sources]
).astype(np.int32)
if self._homogeneous: # homogeneous delays
self._insert_homogeneous(self._delays[0], indices)
elif self._offsets is None: # vectorise over synaptic events
# there are no precomputed offsets, this is the case
# (in particular) when there are dynamic delays
self._insert(self._delays[indices], indices)
else: # offsets are precomputed
self._insert(self._delays[indices], indices, self._offsets[indices])
|
https://github.com/brian-team/brian2/issues/371
|
SG = SpikeGeneratorGroup(1, [0], [0*ms])
G = NeuronGroup(1, 'v:1')
S = Synapses(SG, G, pre='v+=1')
run(0.1*ms)
Traceback (most recent call last):
...
File "/home/marcel/programming/brian2/brian2/synapses/spikequeue.py", line 254, in push
self._insert_homogeneous(self._delays[0], indices)
IndexError: index 0 is out of bounds for axis 0 with size 0
|
IndexError
|
def initialise_queue(self):
if self.synapse_sources.get_len() == 0:
logger.warn(
(
"Synapses object '%s' does not have any synapses. Did "
"you forget a 'connect'?"
)
% self.synapses.name,
"no_synapses",
once=True,
)
if self.queue is None:
self.queue = get_device().spike_queue(self.source.start, self.source.stop)
# Update the dt (might have changed between runs)
self.queue.prepare(
self._delays.get_value(),
self.source.clock.dt_,
self.synapse_sources.get_value(),
)
if (
len(
set([self.source.clock.dt_, self.synapses.clock.dt_, self.target.clock.dt_])
)
> 1
):
logger.warn(
(
"Note that the synaptic pathway '{pathway}' will run on the "
"clock of the group '{source}' using a dt of {dt}. Either "
"the Synapses object '{synapses}' or the target '{target}' "
"(or both) are using a different dt. This might lead to "
"unexpected results. In particular, all delays will be rounded to "
"multiples of {dt}. If in doubt, try to ensure that "
"'{source}', '{synapses}', and '{target}' use the "
"same dt."
).format(
pathway=self.name,
source=self.source.name,
target=self.target.name,
dt=self.source.clock.dt,
synapses=self.synapses.name,
),
"synapses_dt_mismatch",
once=True,
)
|
def initialise_queue(self):
if self.queue is None:
self.queue = get_device().spike_queue(self.source.start, self.source.stop)
# Update the dt (might have changed between runs)
self.queue.prepare(
self._delays.get_value(),
self.source.clock.dt_,
self.synapse_sources.get_value(),
)
if (
len(
set([self.source.clock.dt_, self.synapses.clock.dt_, self.target.clock.dt_])
)
> 1
):
logger.warn(
(
"Note that the synaptic pathway '{pathway}' will run on the "
"clock of the group '{source}' using a dt of {dt}. Either "
"the Synapses object '{synapses}' or the target '{target}' "
"(or both) are using a different dt. This might lead to "
"unexpected results. In particular, all delays will be rounded to "
"multiples of {dt}. If in doubt, try to ensure that "
"'{source}', '{synapses}', and '{target}' use the "
"same dt."
).format(
pathway=self.name,
source=self.source.name,
target=self.target.name,
dt=self.source.clock.dt,
synapses=self.synapses.name,
),
"synapses_dt_mismatch",
once=True,
)
|
https://github.com/brian-team/brian2/issues/371
|
SG = SpikeGeneratorGroup(1, [0], [0*ms])
G = NeuronGroup(1, 'v:1')
S = Synapses(SG, G, pre='v+=1')
run(0.1*ms)
Traceback (most recent call last):
...
File "/home/marcel/programming/brian2/brian2/synapses/spikequeue.py", line 254, in push
self._insert_homogeneous(self._delays[0], indices)
IndexError: index 0 is out of bounds for axis 0 with size 0
|
IndexError
|
def __call__(self, engine: Engine) -> None:
"""
This method assumes self.batch_transform will extract metadata from the input batch.
Args:
engine: Ignite Engine, it can be a trainer, validator or evaluator.
"""
_meta_data = self.batch_transform(engine.state.batch)
if Key.FILENAME_OR_OBJ in _meta_data:
# all gather filenames across ranks, only filenames are necessary
_meta_data = {
Key.FILENAME_OR_OBJ: string_list_all_gather(_meta_data[Key.FILENAME_OR_OBJ])
}
# all gather predictions across ranks
_engine_output = evenly_divisible_all_gather(
self.output_transform(engine.state.output)
)
if self._expected_rank:
self.saver.save_batch(_engine_output, _meta_data)
|
def __call__(self, engine: Engine) -> None:
"""
This method assumes self.batch_transform will extract metadata from the input batch.
Args:
engine: Ignite Engine, it can be a trainer, validator or evaluator.
"""
_meta_data = self.batch_transform(engine.state.batch)
if Key.FILENAME_OR_OBJ in _meta_data:
# all gather filenames across ranks
_meta_data[Key.FILENAME_OR_OBJ] = string_list_all_gather(
_meta_data[Key.FILENAME_OR_OBJ]
)
# all gather predictions across ranks
_engine_output = evenly_divisible_all_gather(
self.output_transform(engine.state.output)
)
if self._expected_rank:
self.saver.save_batch(_engine_output, _meta_data)
|
https://github.com/Project-MONAI/MONAI/issues/1570
|
2021-02-09 02:12:24,253 - ignite.engine.engine.SupervisedEvaluator - INFO - Engine run resuming from iteration 0, epoch 0 until 1 epochs
2021-02-09 02:12:24,436 - ignite.engine.engine.SupervisedEvaluator - INFO - Restored all variables from /home/madil/dlmed/problems/pt_mmars/classification_chestxray_ea2/commands/../models/model.pt
2021-02-09 02:12:29,927 - ignite.engine.engine.SupervisedEvaluator - ERROR - Current run is terminating due to exception: list index out of range.
2021-02-09 02:12:29,928 - ignite.engine.engine.SupervisedEvaluator - ERROR - Exception: list index out of range
Traceback (most recent call last):
File "/opt/conda/lib/python3.6/site-packages/ignite/engine/engine.py", line 812, in _run_once_on_dataset
self._fire_event(Events.ITERATION_COMPLETED)
File "/opt/conda/lib/python3.6/site-packages/ignite/engine/engine.py", line 423, in _fire_event
func(*first, *(event_args + others), **kwargs)
File "/opt/monai/monai/handlers/classification_saver.py", line 97, in __call__
self.saver.save_batch(_engine_output, _meta_data)
File "/opt/monai/monai/data/csv_saver.py", line 95, in save_batch
self.save(data, {k: meta_data[k][i] for k in meta_data} if meta_data else None)
File "/opt/monai/monai/data/csv_saver.py", line 95, in <dictcomp>
self.save(data, {k: meta_data[k][i] for k in meta_data} if meta_data else None)
IndexError: list index out of range
|
IndexError
|
def string_list_all_gather(strings: List[str], delimiter: str = "\t") -> List[str]:
"""
Utility function for distributed data parallel to all gather a list of strings.
Args:
strings: a list of strings to all gather.
delimiter: use the delimiter to join the string list to be a long string,
then all gather across ranks and split to a list. default to "\t".
"""
if idist.get_world_size() <= 1:
return strings
_joined = delimiter.join(strings)
if get_torch_version_tuple() > (1, 6, 0):
# all gather across all ranks
_joined = delimiter.join(idist.all_gather(_joined))
else:
raise RuntimeError("string all_gather can not be supported in PyTorch < 1.7.0.")
return _joined.split(delimiter)
|
def string_list_all_gather(strings: List[str], delimiter: str = "\t") -> List[str]:
"""
Utility function for distributed data parallel to all gather a list of strings.
Args:
strings: a list of strings to all gather.
delimiter: use the delimiter to join the string list to be a long string,
then all gather across ranks and split to a list. default to "\t".
"""
if idist.get_world_size() <= 1:
return strings
_joined = delimiter.join(strings)
if get_torch_version_tuple() > (1, 6, 0):
# all gather across all ranks
_joined = delimiter.join(idist.all_gather(_joined))
else:
raise RuntimeError(
"MetricsSaver can not save metric details in distributed mode with PyTorch < 1.7.0."
)
return _joined.split(delimiter)
|
https://github.com/Project-MONAI/MONAI/issues/1570
|
2021-02-09 02:12:24,253 - ignite.engine.engine.SupervisedEvaluator - INFO - Engine run resuming from iteration 0, epoch 0 until 1 epochs
2021-02-09 02:12:24,436 - ignite.engine.engine.SupervisedEvaluator - INFO - Restored all variables from /home/madil/dlmed/problems/pt_mmars/classification_chestxray_ea2/commands/../models/model.pt
2021-02-09 02:12:29,927 - ignite.engine.engine.SupervisedEvaluator - ERROR - Current run is terminating due to exception: list index out of range.
2021-02-09 02:12:29,928 - ignite.engine.engine.SupervisedEvaluator - ERROR - Exception: list index out of range
Traceback (most recent call last):
File "/opt/conda/lib/python3.6/site-packages/ignite/engine/engine.py", line 812, in _run_once_on_dataset
self._fire_event(Events.ITERATION_COMPLETED)
File "/opt/conda/lib/python3.6/site-packages/ignite/engine/engine.py", line 423, in _fire_event
func(*first, *(event_args + others), **kwargs)
File "/opt/monai/monai/handlers/classification_saver.py", line 97, in __call__
self.saver.save_batch(_engine_output, _meta_data)
File "/opt/monai/monai/data/csv_saver.py", line 95, in save_batch
self.save(data, {k: meta_data[k][i] for k in meta_data} if meta_data else None)
File "/opt/monai/monai/data/csv_saver.py", line 95, in <dictcomp>
self.save(data, {k: meta_data[k][i] for k in meta_data} if meta_data else None)
IndexError: list index out of range
|
IndexError
|
def __call__(self, data):
"""
Raises:
KeyError: When a key in ``self.names`` already exists in ``data``.
"""
d = dict(data)
for key, new_key in zip(self.keys * self.times, self.names):
if new_key in d:
raise KeyError(f"Key {new_key} already exists in data.")
if type(d[key]) == torch.Tensor:
d[new_key] = d[key].detach().clone()
else:
d[new_key] = copy.deepcopy(d[key])
return d
|
def __call__(self, data):
"""
Raises:
KeyError: When a key in ``self.names`` already exists in ``data``.
"""
d = dict(data)
for key, new_key in zip(self.keys * self.times, self.names):
if new_key in d:
raise KeyError(f"Key {new_key} already exists in data.")
d[new_key] = copy.deepcopy(d[key])
return d
|
https://github.com/Project-MONAI/MONAI/issues/1178
|
ERROR - Exception: Applying transform <monai.transforms.compose.Compose object at 0x7f0700e9deb8>.
Traceback (most recent call last):
File "/home/madil/dlmed/code/MONAI/monai/transforms/utils.py", line 309, in apply_transform
return transform(data)
File "/home/madil/dlmed/code/MONAI/monai/transforms/utility/dictionary.py", line 406, in __call__
d[new_key] = copy.deepcopy(d[key])
File "/opt/conda/lib/python3.6/copy.py", line 161, in deepcopy
y = copier(memo)
File "/opt/conda/lib/python3.6/site-packages/torch/tensor.py", line 38, in __deepcopy__
raise RuntimeError("Only Tensors created explicitly by the user "
RuntimeError: Only Tensors created explicitly by the user (graph leaves) support the deepcopy protocol at the moment
|
RuntimeError
|
def __init__(
self,
output_dir: str = "./",
output_postfix: str = "seg",
output_ext: str = ".nii.gz",
resample: bool = True,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
align_corners: bool = False,
dtype: Optional[np.dtype] = np.float64,
) -> None:
"""
Args:
output_dir: output image directory.
output_postfix: a string appended to all output file names.
output_ext: output file extension name.
resample: whether to resample before saving the data array.
mode: {``"bilinear"``, ``"nearest"``}
This option is used when ``resample = True``.
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
This option is used when ``resample = True``.
Padding mode for outside grid values. Defaults to ``"border"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Geometrically, we consider the pixels of the input as squares rather than points.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: data type for resampling computation. Defaults to ``np.float64`` for best precision.
If None, use the data type of input data. To be compatible with other modules,
the output data type is always ``np.float32``.
"""
self.output_dir = output_dir
self.output_postfix = output_postfix
self.output_ext = output_ext
self.resample = resample
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.align_corners = align_corners
self.dtype = dtype
self._data_index = 0
|
def __init__(
self,
output_dir: str = "./",
output_postfix: str = "seg",
output_ext: str = ".nii.gz",
resample: bool = True,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
dtype: Optional[np.dtype] = None,
) -> None:
"""
Args:
output_dir: output image directory.
output_postfix: a string appended to all output file names.
output_ext: output file extension name.
resample: whether to resample before saving the data array.
mode: {``"bilinear"``, ``"nearest"``}
This option is used when ``resample = True``.
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
This option is used when ``resample = True``.
Padding mode for outside grid values. Defaults to ``"border"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: convert the image data to save to this data type.
If None, keep the original type of data.
"""
self.output_dir = output_dir
self.output_postfix = output_postfix
self.output_ext = output_ext
self.resample = resample
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.dtype = dtype
self._data_index = 0
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def save(
self, data: Union[torch.Tensor, np.ndarray], meta_data: Optional[Dict] = None
) -> None:
"""
Save data into a Nifti file.
The meta_data could optionally have the following keys:
- ``'filename_or_obj'`` -- for output file name creation, corresponding to filename or object.
- ``'original_affine'`` -- for data orientation handling, defaulting to an identity matrix.
- ``'affine'`` -- for data output affine, defaulting to an identity matrix.
- ``'spatial_shape'`` -- for data output shape.
When meta_data is specified, the saver will try to resample batch data from the space
defined by "affine" to the space defined by "original_affine".
If meta_data is None, use the default index (starting from 0) as the filename.
Args:
data: target data content that to be saved as a NIfTI format file.
Assuming the data shape starts with a channel dimension and followed by spatial dimensions.
meta_data: the meta data information corresponding to the data.
See Also
:py:meth:`monai.data.nifti_writer.write_nifti`
"""
filename = meta_data["filename_or_obj"] if meta_data else str(self._data_index)
self._data_index += 1
original_affine = meta_data.get("original_affine", None) if meta_data else None
affine = meta_data.get("affine", None) if meta_data else None
spatial_shape = meta_data.get("spatial_shape", None) if meta_data else None
if torch.is_tensor(data):
data = data.detach().cpu().numpy()
filename = create_file_basename(self.output_postfix, filename, self.output_dir)
filename = f"{filename}{self.output_ext}"
# change data shape to be (channel, h, w, d)
while len(data.shape) < 4:
data = np.expand_dims(data, -1)
# change data to "channel last" format and write to nifti format file
data = np.moveaxis(data, 0, -1)
write_nifti(
data,
file_name=filename,
affine=affine,
target_affine=original_affine,
resample=self.resample,
output_spatial_shape=spatial_shape,
mode=self.mode,
padding_mode=self.padding_mode,
align_corners=self.align_corners,
dtype=self.dtype,
)
|
def save(
self, data: Union[torch.Tensor, np.ndarray], meta_data: Optional[Dict] = None
) -> None:
"""
Save data into a Nifti file.
The meta_data could optionally have the following keys:
- ``'filename_or_obj'`` -- for output file name creation, corresponding to filename or object.
- ``'original_affine'`` -- for data orientation handling, defaulting to an identity matrix.
- ``'affine'`` -- for data output affine, defaulting to an identity matrix.
- ``'spatial_shape'`` -- for data output shape.
When meta_data is specified, the saver will try to resample batch data from the space
defined by "affine" to the space defined by "original_affine".
If meta_data is None, use the default index (starting from 0) as the filename.
Args:
data: target data content that to be saved as a NIfTI format file.
Assuming the data shape starts with a channel dimension and followed by spatial dimensions.
meta_data: the meta data information corresponding to the data.
See Also
:py:meth:`monai.data.nifti_writer.write_nifti`
"""
filename = meta_data["filename_or_obj"] if meta_data else str(self._data_index)
self._data_index += 1
original_affine = meta_data.get("original_affine", None) if meta_data else None
affine = meta_data.get("affine", None) if meta_data else None
spatial_shape = meta_data.get("spatial_shape", None) if meta_data else None
if torch.is_tensor(data):
data = data.detach().cpu().numpy()
filename = create_file_basename(self.output_postfix, filename, self.output_dir)
filename = f"{filename}{self.output_ext}"
# change data shape to be (channel, h, w, d)
while len(data.shape) < 4:
data = np.expand_dims(data, -1)
# change data to "channel last" format and write to nifti format file
data = np.moveaxis(data, 0, -1)
write_nifti(
data,
file_name=filename,
affine=affine,
target_affine=original_affine,
resample=self.resample,
output_spatial_shape=spatial_shape,
mode=self.mode,
padding_mode=self.padding_mode,
dtype=self.dtype or data.dtype,
)
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def write_nifti(
data: np.ndarray,
file_name: str,
affine: Optional[np.ndarray] = None,
target_affine: Optional[np.ndarray] = None,
resample: bool = True,
output_spatial_shape: Optional[Sequence[int]] = None,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
align_corners: bool = False,
dtype: Optional[np.dtype] = np.float64,
) -> None:
"""
Write numpy data into NIfTI files to disk. This function converts data
into the coordinate system defined by `target_affine` when `target_affine`
is specified.
If the coordinate transform between `affine` and `target_affine` could be
achieved by simply transposing and flipping `data`, no resampling will
happen. otherwise this function will resample `data` using the coordinate
transform computed from `affine` and `target_affine`. Note that the shape
of the resampled `data` may subject to some rounding errors. For example,
resampling a 20x20 pixel image from pixel size (1.5, 1.5)-mm to (3.0,
3.0)-mm space will return a 10x10-pixel image. However, resampling a
20x20-pixel image from pixel size (2.0, 2.0)-mm to (3.0, 3.0)-mma space
will output a 14x14-pixel image, where the image shape is rounded from
13.333x13.333 pixels. In this case `output_spatial_shape` could be specified so
that this function writes image data to a designated shape.
When `affine` and `target_affine` are None, the data will be saved with an
identity matrix as the image affine.
This function assumes the NIfTI dimension notations.
Spatially it supports up to three dimensions, that is, H, HW, HWD for
1D, 2D, 3D respectively.
When saving multiple time steps or multiple channels `data`, time and/or
modality axes should be appended after the first three dimensions. For
example, shape of 2D eight-class segmentation probabilities to be saved
could be `(64, 64, 1, 8)`. Also, data in shape (64, 64, 8), (64, 64, 8, 1)
will be considered as a single-channel 3D image.
Args:
data: input data to write to file.
file_name: expected file name that saved on disk.
affine: the current affine of `data`. Defaults to `np.eye(4)`
target_affine: before saving
the (`data`, `affine`) as a Nifti1Image,
transform the data into the coordinates defined by `target_affine`.
resample: whether to run resampling when the target affine
could not be achieved by swapping/flipping data axes.
output_spatial_shape: spatial shape of the output image.
This option is used when resample = True.
mode: {``"bilinear"``, ``"nearest"``}
This option is used when ``resample = True``.
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
This option is used when ``resample = True``.
Padding mode for outside grid values. Defaults to ``"border"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Geometrically, we consider the pixels of the input as squares rather than points.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: data type for resampling computation. Defaults to ``np.float64`` for best precision.
If None, use the data type of input data. To be compatible with other modules,
the output data type is always ``np.float32``.
"""
assert isinstance(data, np.ndarray), "input data must be numpy array."
dtype = dtype or data.dtype
sr = min(data.ndim, 3)
if affine is None:
affine = np.eye(4, dtype=np.float64)
affine = to_affine_nd(sr, affine)
if target_affine is None:
target_affine = affine
target_affine = to_affine_nd(sr, target_affine)
if np.allclose(affine, target_affine, atol=1e-3):
# no affine changes, save (data, affine)
results_img = nib.Nifti1Image(
data.astype(np.float32), to_affine_nd(3, target_affine)
)
nib.save(results_img, file_name)
return
# resolve orientation
start_ornt = nib.orientations.io_orientation(affine)
target_ornt = nib.orientations.io_orientation(target_affine)
ornt_transform = nib.orientations.ornt_transform(start_ornt, target_ornt)
data_shape = data.shape
data = nib.orientations.apply_orientation(data, ornt_transform)
_affine = affine @ nib.orientations.inv_ornt_aff(ornt_transform, data_shape)
if np.allclose(_affine, target_affine, atol=1e-3) or not resample:
results_img = nib.Nifti1Image(
data.astype(np.float32), to_affine_nd(3, target_affine)
)
nib.save(results_img, file_name)
return
# need resampling
affine_xform = AffineTransform(
normalized=False,
mode=mode,
padding_mode=padding_mode,
align_corners=align_corners,
reverse_indexing=True,
)
transform = np.linalg.inv(_affine) @ target_affine
if output_spatial_shape is None:
output_spatial_shape, _ = compute_shape_offset(
data.shape, _affine, target_affine
)
output_spatial_shape_ = list(output_spatial_shape)
if data.ndim > 3: # multi channel, resampling each channel
while len(output_spatial_shape_) < 3:
output_spatial_shape_ = output_spatial_shape_ + [1]
spatial_shape, channel_shape = data.shape[:3], data.shape[3:]
data_ = data.reshape(list(spatial_shape) + [-1])
data_ = np.moveaxis(data_, -1, 0) # channel first for pytorch
data_ = affine_xform(
torch.as_tensor(np.ascontiguousarray(data_).astype(dtype)).unsqueeze(0),
torch.as_tensor(np.ascontiguousarray(transform).astype(dtype)),
spatial_size=output_spatial_shape_[:3],
)
data_ = data_.squeeze(0).detach().cpu().numpy()
data_ = np.moveaxis(data_, 0, -1) # channel last for nifti
data_ = data_.reshape(list(data_.shape[:3]) + list(channel_shape))
else: # single channel image, need to expand to have batch and channel
while len(output_spatial_shape_) < len(data.shape):
output_spatial_shape_ = output_spatial_shape_ + [1]
data_ = affine_xform(
torch.as_tensor(np.ascontiguousarray(data).astype(dtype)[None, None]),
torch.as_tensor(np.ascontiguousarray(transform).astype(dtype)),
spatial_size=output_spatial_shape_[: len(data.shape)],
)
data_ = data_.squeeze(0).squeeze(0).detach().cpu().numpy()
results_img = nib.Nifti1Image(
data_.astype(np.float32), to_affine_nd(3, target_affine)
)
nib.save(results_img, file_name)
return
|
def write_nifti(
data: np.ndarray,
file_name: str,
affine: Optional[np.ndarray] = None,
target_affine: Optional[np.ndarray] = None,
resample: bool = True,
output_spatial_shape: Optional[Sequence[int]] = None,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
dtype: Optional[np.dtype] = None,
) -> None:
"""
Write numpy data into NIfTI files to disk. This function converts data
into the coordinate system defined by `target_affine` when `target_affine`
is specified.
If the coordinate transform between `affine` and `target_affine` could be
achieved by simply transposing and flipping `data`, no resampling will
happen. otherwise this function will resample `data` using the coordinate
transform computed from `affine` and `target_affine`. Note that the shape
of the resampled `data` may subject to some rounding errors. For example,
resampling a 20x20 pixel image from pixel size (1.5, 1.5)-mm to (3.0,
3.0)-mm space will return a 10x10-pixel image. However, resampling a
20x20-pixel image from pixel size (2.0, 2.0)-mm to (3.0, 3.0)-mma space
will output a 14x14-pixel image, where the image shape is rounded from
13.333x13.333 pixels. In this case `output_spatial_shape` could be specified so
that this function writes image data to a designated shape.
When `affine` and `target_affine` are None, the data will be saved with an
identity matrix as the image affine.
This function assumes the NIfTI dimension notations.
Spatially it supports up to three dimensions, that is, H, HW, HWD for
1D, 2D, 3D respectively.
When saving multiple time steps or multiple channels `data`, time and/or
modality axes should be appended after the first three dimensions. For
example, shape of 2D eight-class segmentation probabilities to be saved
could be `(64, 64, 1, 8)`. Also, data in shape (64, 64, 8), (64, 64, 8, 1)
will be considered as a single-channel 3D image.
Args:
data: input data to write to file.
file_name: expected file name that saved on disk.
affine: the current affine of `data`. Defaults to `np.eye(4)`
target_affine: before saving
the (`data`, `affine`) as a Nifti1Image,
transform the data into the coordinates defined by `target_affine`.
resample: whether to run resampling when the target affine
could not be achieved by swapping/flipping data axes.
output_spatial_shape: spatial shape of the output image.
This option is used when resample = True.
mode: {``"bilinear"``, ``"nearest"``}
This option is used when ``resample = True``.
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
This option is used when ``resample = True``.
Padding mode for outside grid values. Defaults to ``"border"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: convert the image to save to this data type.
"""
assert isinstance(data, np.ndarray), "input data must be numpy array."
sr = min(data.ndim, 3)
if affine is None:
affine = np.eye(4, dtype=np.float64)
affine = to_affine_nd(sr, affine)
if target_affine is None:
target_affine = affine
target_affine = to_affine_nd(sr, target_affine)
if np.allclose(affine, target_affine, atol=1e-3):
# no affine changes, save (data, affine)
results_img = nib.Nifti1Image(
data.astype(dtype), to_affine_nd(3, target_affine)
)
nib.save(results_img, file_name)
return
# resolve orientation
start_ornt = nib.orientations.io_orientation(affine)
target_ornt = nib.orientations.io_orientation(target_affine)
ornt_transform = nib.orientations.ornt_transform(start_ornt, target_ornt)
data_shape = data.shape
data = nib.orientations.apply_orientation(data, ornt_transform)
_affine = affine @ nib.orientations.inv_ornt_aff(ornt_transform, data_shape)
if np.allclose(_affine, target_affine, atol=1e-3) or not resample:
results_img = nib.Nifti1Image(
data.astype(dtype), to_affine_nd(3, target_affine)
)
nib.save(results_img, file_name)
return
# need resampling
affine_xform = AffineTransform(
normalized=False,
mode=mode,
padding_mode=padding_mode,
align_corners=True,
reverse_indexing=True,
)
transform = np.linalg.inv(_affine) @ target_affine
if output_spatial_shape is None:
output_spatial_shape, _ = compute_shape_offset(
data.shape, _affine, target_affine
)
output_spatial_shape_ = list(output_spatial_shape)
if data.ndim > 3: # multi channel, resampling each channel
while len(output_spatial_shape_) < 3:
output_spatial_shape_ = output_spatial_shape_ + [1]
spatial_shape, channel_shape = data.shape[:3], data.shape[3:]
data_ = data.reshape(list(spatial_shape) + [-1])
data_ = np.moveaxis(data_, -1, 0) # channel first for pytorch
data_ = affine_xform(
torch.from_numpy(data_.astype(np.float64)).unsqueeze(0),
torch.from_numpy(transform.astype(np.float64)),
spatial_size=output_spatial_shape_[:3],
)
data_ = data_.squeeze(0).detach().cpu().numpy()
data_ = np.moveaxis(data_, 0, -1) # channel last for nifti
data_ = data_.reshape(list(data_.shape[:3]) + list(channel_shape))
else: # single channel image, need to expand to have batch and channel
while len(output_spatial_shape_) < len(data.shape):
output_spatial_shape_ = output_spatial_shape_ + [1]
data_ = affine_xform(
torch.from_numpy((data.astype(np.float64))[None, None]),
torch.from_numpy(transform.astype(np.float64)),
spatial_size=output_spatial_shape_[: len(data.shape)],
)
data_ = data_.squeeze(0).squeeze(0).detach().cpu().numpy()
dtype = dtype or data.dtype
results_img = nib.Nifti1Image(data_.astype(dtype), to_affine_nd(3, target_affine))
nib.save(results_img, file_name)
return
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def __init__(
self,
pixdim: Union[Sequence[float], float],
diagonal: bool = False,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
align_corners: bool = False,
dtype: Optional[np.dtype] = np.float64,
) -> None:
"""
Args:
pixdim: output voxel spacing.
diagonal: whether to resample the input to have a diagonal affine matrix.
If True, the input data is resampled to the following affine::
np.diag((pixdim_0, pixdim_1, ..., pixdim_n, 1))
This effectively resets the volume to the world coordinate system (RAS+ in nibabel).
The original orientation, rotation, shearing are not preserved.
If False, this transform preserves the axes orientation, orthogonal rotation and
translation components from the original affine. This option will not flip/swap axes
of the original data.
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``"border"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Geometrically, we consider the pixels of the input as squares rather than points.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: data type for resampling computation. Defaults to ``np.float64`` for best precision.
If None, use the data type of input data. To be compatible with other modules,
the output data type is always ``np.float32``.
"""
self.pixdim = np.array(ensure_tuple(pixdim), dtype=np.float64)
self.diagonal = diagonal
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.align_corners = align_corners
self.dtype = dtype
|
def __init__(
self,
pixdim: Union[Sequence[float], float],
diagonal: bool = False,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
dtype: Optional[np.dtype] = None,
) -> None:
"""
Args:
pixdim: output voxel spacing.
diagonal: whether to resample the input to have a diagonal affine matrix.
If True, the input data is resampled to the following affine::
np.diag((pixdim_0, pixdim_1, ..., pixdim_n, 1))
This effectively resets the volume to the world coordinate system (RAS+ in nibabel).
The original orientation, rotation, shearing are not preserved.
If False, this transform preserves the axes orientation, orthogonal rotation and
translation components from the original affine. This option will not flip/swap axes
of the original data.
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``"border"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: output array data type. Defaults to ``np.float32``.
"""
self.pixdim = np.array(ensure_tuple(pixdim), dtype=np.float64)
self.diagonal = diagonal
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.dtype = dtype
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def __call__(
self,
data_array: np.ndarray,
affine=None,
mode: Optional[Union[GridSampleMode, str]] = None,
padding_mode: Optional[Union[GridSamplePadMode, str]] = None,
align_corners: Optional[bool] = None,
dtype: Optional[np.dtype] = None,
):
"""
Args:
data_array: in shape (num_channels, H[, W, ...]).
affine (matrix): (N+1)x(N+1) original affine matrix for spatially ND `data_array`. Defaults to identity.
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``self.mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``self.padding_mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Geometrically, we consider the pixels of the input as squares rather than points.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: data type for resampling computation. Defaults to ``self.dtype``.
If None, use the data type of input data. To be compatible with other modules,
the output data type is always ``np.float32``.
Raises:
ValueError: When ``data_array`` has no spatial dimensions.
ValueError: When ``pixdim`` is nonpositive.
Returns:
data_array (resampled into `self.pixdim`), original pixdim, current pixdim.
"""
_dtype = dtype or self.dtype or data_array.dtype
sr = data_array.ndim - 1
if sr <= 0:
raise ValueError("data_array must have at least one spatial dimension.")
if affine is None:
# default to identity
affine = np.eye(sr + 1, dtype=np.float64)
affine_ = np.eye(sr + 1, dtype=np.float64)
else:
affine_ = to_affine_nd(sr, affine)
out_d = self.pixdim[:sr]
if out_d.size < sr:
out_d = np.append(out_d, [1.0] * (out_d.size - sr))
if np.any(out_d <= 0):
raise ValueError(f"pixdim must be positive, got {out_d}.")
# compute output affine, shape and offset
new_affine = zoom_affine(affine_, out_d, diagonal=self.diagonal)
output_shape, offset = compute_shape_offset(
data_array.shape[1:], affine_, new_affine
)
new_affine[:sr, -1] = offset[:sr]
transform = np.linalg.inv(affine_) @ new_affine
# adapt to the actual rank
transform_ = to_affine_nd(sr, transform)
# no resampling if it's identity transform
if np.allclose(transform_, np.diag(np.ones(len(transform_))), atol=1e-3):
output_data = data_array.copy().astype(np.float32)
new_affine = to_affine_nd(affine, new_affine)
return output_data, affine, new_affine
# resample
affine_xform = AffineTransform(
normalized=False,
mode=mode or self.mode,
padding_mode=padding_mode or self.padding_mode,
align_corners=self.align_corners if align_corners is None else align_corners,
reverse_indexing=True,
)
output_data = affine_xform(
# AffineTransform requires a batch dim
torch.as_tensor(np.ascontiguousarray(data_array).astype(_dtype)).unsqueeze(0),
torch.as_tensor(np.ascontiguousarray(transform_).astype(_dtype)),
spatial_size=output_shape,
)
output_data = output_data.squeeze(0).detach().cpu().numpy().astype(np.float32)
new_affine = to_affine_nd(affine, new_affine)
return output_data, affine, new_affine
|
def __call__(
self,
data_array: np.ndarray,
affine=None,
mode: Optional[Union[GridSampleMode, str]] = None,
padding_mode: Optional[Union[GridSamplePadMode, str]] = None,
dtype: Optional[np.dtype] = None,
):
"""
Args:
data_array: in shape (num_channels, H[, W, ...]).
affine (matrix): (N+1)x(N+1) original affine matrix for spatially ND `data_array`. Defaults to identity.
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``self.mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``self.padding_mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: output array data type. Defaults to ``self.dtype``.
Raises:
ValueError: When ``data_array`` has no spatial dimensions.
ValueError: When ``pixdim`` is nonpositive.
Returns:
data_array (resampled into `self.pixdim`), original pixdim, current pixdim.
"""
sr = data_array.ndim - 1
if sr <= 0:
raise ValueError("data_array must have at least one spatial dimension.")
if affine is None:
# default to identity
affine = np.eye(sr + 1, dtype=np.float64)
affine_ = np.eye(sr + 1, dtype=np.float64)
else:
affine_ = to_affine_nd(sr, affine)
out_d = self.pixdim[:sr]
if out_d.size < sr:
out_d = np.append(out_d, [1.0] * (out_d.size - sr))
if np.any(out_d <= 0):
raise ValueError(f"pixdim must be positive, got {out_d}.")
# compute output affine, shape and offset
new_affine = zoom_affine(affine_, out_d, diagonal=self.diagonal)
output_shape, offset = compute_shape_offset(
data_array.shape[1:], affine_, new_affine
)
new_affine[:sr, -1] = offset[:sr]
transform = np.linalg.inv(affine_) @ new_affine
# adapt to the actual rank
transform_ = to_affine_nd(sr, transform)
_dtype = dtype or self.dtype or np.float32
# no resampling if it's identity transform
if np.allclose(transform_, np.diag(np.ones(len(transform_))), atol=1e-3):
output_data = data_array.copy().astype(_dtype)
new_affine = to_affine_nd(affine, new_affine)
return output_data, affine, new_affine
# resample
affine_xform = AffineTransform(
normalized=False,
mode=mode or self.mode,
padding_mode=padding_mode or self.padding_mode,
align_corners=True,
reverse_indexing=True,
)
output_data = affine_xform(
torch.from_numpy((data_array.astype(np.float64))).unsqueeze(
0
), # AffineTransform requires a batch dim
torch.from_numpy(transform_.astype(np.float64)),
spatial_size=output_shape,
)
output_data = output_data.squeeze(0).detach().cpu().numpy().astype(_dtype)
new_affine = to_affine_nd(affine, new_affine)
return output_data, affine, new_affine
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def __init__(
self,
angle: Union[Sequence[float], float],
keep_size: bool = True,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
align_corners: bool = False,
dtype: Optional[np.dtype] = np.float64,
) -> None:
self.angle = angle
self.keep_size = keep_size
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.align_corners = align_corners
self.dtype = dtype
|
def __init__(
self,
angle: Union[Sequence[float], float],
keep_size: bool = True,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
align_corners: bool = False,
) -> None:
self.angle = angle
self.keep_size = keep_size
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.align_corners = align_corners
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def __call__(
self,
img: np.ndarray,
mode: Optional[Union[GridSampleMode, str]] = None,
padding_mode: Optional[Union[GridSamplePadMode, str]] = None,
align_corners: Optional[bool] = None,
dtype: Optional[np.dtype] = None,
) -> np.ndarray:
"""
Args:
img: channel first array, must have shape: [chns, H, W] or [chns, H, W, D].
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``self.mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``self.padding_mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Defaults to ``self.align_corners``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Defaults to ``self.align_corners``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: data type for resampling computation. Defaults to ``self.dtype``.
If None, use the data type of input data. To be compatible with other modules,
the output data type is always ``np.float32``.
Raises:
ValueError: When ``img`` spatially is not one of [2D, 3D].
"""
_dtype = dtype or self.dtype or img.dtype
im_shape = np.asarray(img.shape[1:]) # spatial dimensions
input_ndim = len(im_shape)
if input_ndim not in (2, 3):
raise ValueError(
f"Unsupported img dimension: {input_ndim}, available options are [2, 3]."
)
_angle = ensure_tuple_rep(self.angle, 1 if input_ndim == 2 else 3)
_rad = np.deg2rad(_angle)
transform = create_rotate(input_ndim, _rad)
shift = create_translate(input_ndim, (im_shape - 1) / 2)
if self.keep_size:
output_shape = im_shape
else:
corners = np.asarray(
np.meshgrid(*[(0, dim) for dim in im_shape], indexing="ij")
).reshape((len(im_shape), -1))
corners = transform[:-1, :-1] @ corners
output_shape = (corners.ptp(axis=1) + 0.5).astype(int)
shift_1 = create_translate(input_ndim, -(output_shape - 1) / 2)
transform = shift @ transform @ shift_1
xform = AffineTransform(
normalized=False,
mode=mode or self.mode,
padding_mode=padding_mode or self.padding_mode,
align_corners=self.align_corners if align_corners is None else align_corners,
reverse_indexing=True,
)
output = xform(
torch.as_tensor(np.ascontiguousarray(img).astype(_dtype)).unsqueeze(0),
torch.as_tensor(np.ascontiguousarray(transform).astype(_dtype)),
spatial_size=output_shape,
)
output = output.squeeze(0).detach().cpu().numpy().astype(np.float32)
return output
|
def __call__(
self,
img: np.ndarray,
mode: Optional[Union[GridSampleMode, str]] = None,
padding_mode: Optional[Union[GridSamplePadMode, str]] = None,
align_corners: Optional[bool] = None,
) -> np.ndarray:
"""
Args:
img: channel first array, must have shape: [chns, H, W] or [chns, H, W, D].
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``self.mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``self.padding_mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Defaults to ``self.align_corners``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Defaults to ``self.align_corners``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
Raises:
ValueError: When ``img`` spatially is not one of [2D, 3D].
"""
im_shape = np.asarray(img.shape[1:]) # spatial dimensions
input_ndim = len(im_shape)
if input_ndim not in (2, 3):
raise ValueError(
f"Unsupported img dimension: {input_ndim}, available options are [2, 3]."
)
_angle = ensure_tuple_rep(self.angle, 1 if input_ndim == 2 else 3)
_rad = np.deg2rad(_angle)
transform = create_rotate(input_ndim, _rad)
shift = create_translate(input_ndim, (im_shape - 1) / 2)
if self.keep_size:
output_shape = im_shape
else:
corners = np.asarray(
np.meshgrid(*[(0, dim) for dim in im_shape], indexing="ij")
).reshape((len(im_shape), -1))
corners = transform[:-1, :-1] @ corners
output_shape = (corners.ptp(axis=1) + 0.5).astype(int)
shift_1 = create_translate(input_ndim, -(output_shape - 1) / 2)
transform = shift @ transform @ shift_1
_dtype = img.dtype
xform = AffineTransform(
normalized=False,
mode=mode or self.mode,
padding_mode=padding_mode or self.padding_mode,
align_corners=self.align_corners if align_corners is None else align_corners,
reverse_indexing=True,
)
output = xform(
torch.from_numpy(img.astype(np.float64)).unsqueeze(0),
torch.from_numpy(transform.astype(np.float64)),
spatial_size=output_shape,
)
output = output.squeeze(0).detach().cpu().numpy().astype(_dtype)
return output
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def __init__(
self,
range_x: Union[Tuple[float, float], float] = 0.0,
range_y: Union[Tuple[float, float], float] = 0.0,
range_z: Union[Tuple[float, float], float] = 0.0,
prob: float = 0.1,
keep_size: bool = True,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
align_corners: bool = False,
dtype: Optional[np.dtype] = np.float64,
) -> None:
self.range_x = ensure_tuple(range_x)
if len(self.range_x) == 1:
self.range_x = tuple(sorted([-self.range_x[0], self.range_x[0]]))
self.range_y = ensure_tuple(range_y)
if len(self.range_y) == 1:
self.range_y = tuple(sorted([-self.range_y[0], self.range_y[0]]))
self.range_z = ensure_tuple(range_z)
if len(self.range_z) == 1:
self.range_z = tuple(sorted([-self.range_z[0], self.range_z[0]]))
self.prob = prob
self.keep_size = keep_size
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.align_corners = align_corners
self.dtype = dtype
self._do_transform = False
self.x = 0.0
self.y = 0.0
self.z = 0.0
|
def __init__(
self,
range_x: Union[Tuple[float, float], float] = 0.0,
range_y: Union[Tuple[float, float], float] = 0.0,
range_z: Union[Tuple[float, float], float] = 0.0,
prob: float = 0.1,
keep_size: bool = True,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.BORDER,
align_corners: bool = False,
) -> None:
self.range_x = ensure_tuple(range_x)
if len(self.range_x) == 1:
self.range_x = tuple(sorted([-self.range_x[0], self.range_x[0]]))
self.range_y = ensure_tuple(range_y)
if len(self.range_y) == 1:
self.range_y = tuple(sorted([-self.range_y[0], self.range_y[0]]))
self.range_z = ensure_tuple(range_z)
if len(self.range_z) == 1:
self.range_z = tuple(sorted([-self.range_z[0], self.range_z[0]]))
self.prob = prob
self.keep_size = keep_size
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.align_corners = align_corners
self._do_transform = False
self.x = 0.0
self.y = 0.0
self.z = 0.0
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def __call__(
self,
img: np.ndarray,
mode: Optional[Union[GridSampleMode, str]] = None,
padding_mode: Optional[Union[GridSamplePadMode, str]] = None,
align_corners: Optional[bool] = None,
dtype: Optional[np.dtype] = None,
) -> np.ndarray:
"""
Args:
img: channel first array, must have shape 2D: (nchannels, H, W), or 3D: (nchannels, H, W, D).
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``self.mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``self.padding_mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Defaults to ``self.align_corners``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
dtype: data type for resampling computation. Defaults to ``self.dtype``.
If None, use the data type of input data. To be compatible with other modules,
the output data type is always ``np.float32``.
"""
self.randomize()
if not self._do_transform:
return img
rotator = Rotate(
angle=self.x if img.ndim == 3 else (self.x, self.y, self.z),
keep_size=self.keep_size,
mode=mode or self.mode,
padding_mode=padding_mode or self.padding_mode,
align_corners=self.align_corners if align_corners is None else align_corners,
dtype=dtype or self.dtype or img.dtype,
)
return rotator(img)
|
def __call__(
self,
img: np.ndarray,
mode: Optional[Union[GridSampleMode, str]] = None,
padding_mode: Optional[Union[GridSamplePadMode, str]] = None,
align_corners: Optional[bool] = None,
) -> np.ndarray:
"""
Args:
img: channel first array, must have shape 2D: (nchannels, H, W), or 3D: (nchannels, H, W, D).
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``self.mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``self.padding_mode``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: Defaults to ``self.align_corners``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
"""
self.randomize()
if not self._do_transform:
return img
rotator = Rotate(
angle=self.x if img.ndim == 3 else (self.x, self.y, self.z),
keep_size=self.keep_size,
mode=mode or self.mode,
padding_mode=padding_mode or self.padding_mode,
align_corners=self.align_corners if align_corners is None else align_corners,
)
return rotator(img)
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def __init__(
self,
keys: KeysCollection,
pixdim: Sequence[float],
diagonal: bool = False,
mode: GridSampleModeSequence = GridSampleMode.BILINEAR,
padding_mode: GridSamplePadModeSequence = GridSamplePadMode.BORDER,
align_corners: Union[Sequence[bool], bool] = False,
dtype: Optional[Union[Sequence[np.dtype], np.dtype]] = np.float64,
meta_key_postfix: str = "meta_dict",
) -> None:
"""
Args:
pixdim: output voxel spacing.
diagonal: whether to resample the input to have a diagonal affine matrix.
If True, the input data is resampled to the following affine::
np.diag((pixdim_0, pixdim_1, pixdim_2, 1))
This effectively resets the volume to the world coordinate system (RAS+ in nibabel).
The original orientation, rotation, shearing are not preserved.
If False, the axes orientation, orthogonal rotation and
translations components from the original affine will be
preserved in the target affine. This option will not flip/swap
axes against the original ones.
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
It also can be a sequence of string, each element corresponds to a key in ``keys``.
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``"border"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
It also can be a sequence of string, each element corresponds to a key in ``keys``.
align_corners: Geometrically, we consider the pixels of the input as squares rather than points.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
It also can be a sequence of bool, each element corresponds to a key in ``keys``.
dtype: data type for resampling computation. Defaults to ``np.float64`` for best precision.
If None, use the data type of input data. To be compatible with other modules,
the output data type is always ``np.float32``.
It also can be a sequence of np.dtype, each element corresponds to a key in ``keys``.
meta_key_postfix: use `key_{postfix}` to to fetch the meta data according to the key data,
default is `meta_dict`, the meta data is a dictionary object.
For example, to handle key `image`, read/write affine matrices from the
metadata `image_meta_dict` dictionary's `affine` field.
Raises:
TypeError: When ``meta_key_postfix`` is not a ``str``.
"""
super().__init__(keys)
self.spacing_transform = Spacing(pixdim, diagonal=diagonal)
self.mode = ensure_tuple_rep(mode, len(self.keys))
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys))
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys))
self.dtype = ensure_tuple_rep(dtype, len(self.keys))
if not isinstance(meta_key_postfix, str):
raise TypeError(
f"meta_key_postfix must be a str but is {type(meta_key_postfix).__name__}."
)
self.meta_key_postfix = meta_key_postfix
|
def __init__(
self,
keys: KeysCollection,
pixdim: Sequence[float],
diagonal: bool = False,
mode: GridSampleModeSequence = GridSampleMode.BILINEAR,
padding_mode: GridSamplePadModeSequence = GridSamplePadMode.BORDER,
dtype: Optional[Union[Sequence[np.dtype], np.dtype]] = None,
meta_key_postfix: str = "meta_dict",
) -> None:
"""
Args:
pixdim: output voxel spacing.
diagonal: whether to resample the input to have a diagonal affine matrix.
If True, the input data is resampled to the following affine::
np.diag((pixdim_0, pixdim_1, pixdim_2, 1))
This effectively resets the volume to the world coordinate system (RAS+ in nibabel).
The original orientation, rotation, shearing are not preserved.
If False, the axes orientation, orthogonal rotation and
translations components from the original affine will be
preserved in the target affine. This option will not flip/swap
axes against the original ones.
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
It also can be a sequence of string, each element corresponds to a key in ``keys``.
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``"border"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
It also can be a sequence of string, each element corresponds to a key in ``keys``.
dtype: output array data type.
Defaults to None to use input data's dtype. It also can be a sequence of np.dtype,
each element corresponds to a key in ``keys``.
meta_key_postfix: use `key_{postfix}` to to fetch the meta data according to the key data,
default is `meta_dict`, the meta data is a dictionary object.
For example, to handle key `image`, read/write affine matrices from the
metadata `image_meta_dict` dictionary's `affine` field.
Raises:
TypeError: When ``meta_key_postfix`` is not a ``str``.
"""
super().__init__(keys)
self.spacing_transform = Spacing(pixdim, diagonal=diagonal)
self.mode = ensure_tuple_rep(mode, len(self.keys))
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys))
self.dtype = ensure_tuple_rep(dtype, len(self.keys))
if not isinstance(meta_key_postfix, str):
raise TypeError(
f"meta_key_postfix must be a str but is {type(meta_key_postfix).__name__}."
)
self.meta_key_postfix = meta_key_postfix
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
def __call__(self, data):
d = dict(data)
for idx, key in enumerate(self.keys):
meta_data = d[f"{key}_{self.meta_key_postfix}"]
# resample array of each corresponding key
# using affine fetched from d[affine_key]
d[key], _, new_affine = self.spacing_transform(
data_array=d[key],
affine=meta_data["affine"],
mode=self.mode[idx],
padding_mode=self.padding_mode[idx],
align_corners=self.align_corners[idx],
dtype=self.dtype[idx],
)
# set the 'affine' key
meta_data["affine"] = new_affine
return d
|
def __call__(self, data):
d = dict(data)
for idx, key in enumerate(self.keys):
meta_data = d[f"{key}_{self.meta_key_postfix}"]
# resample array of each corresponding key
# using affine fetched from d[affine_key]
d[key], _, new_affine = self.spacing_transform(
data_array=d[key],
affine=meta_data["affine"],
mode=self.mode[idx],
padding_mode=self.padding_mode[idx],
dtype=self.dtype[idx],
)
# set the 'affine' key
meta_data["affine"] = new_affine
return d
|
https://github.com/Project-MONAI/MONAI/issues/832
|
======================================================================
FAIL: test_training (__main__.IntegrationSegmentation3D)
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_integration_segmentation_3d.py", line 257, in test_training
rtol=1e-3,
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 1533, in assert_allclose
verbose=verbose, header=header, equal_nan=equal_nan)
File "/opt/conda/lib/python3.6/site-packages/numpy/testing/_private/utils.py", line 846, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.001, atol=0
Mismatched elements: 6 / 6 (100%)
Max absolute difference: 0.01720129
Max relative difference: 0.04047175
x: array([0.543151, 0.471052, 0.453605, 0.438546, 0.437794, 0.407818])
y: array([0.544673, 0.475109, 0.444963, 0.427036, 0.433381, 0.42502 ])
----------------------------------------------------------------------
Ran 1 test in 92.377s
FAILED (failures=1)
|
AssertionError
|
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