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247,000 | cirruscluster/cirruscluster | cirruscluster/ext/ansible/runner/__init__.py | Runner._copy_module | def _copy_module(self, conn, tmp, module_name, module_args, inject):
''' transfer a module over SFTP, does not run it '''
if module_name.startswith("/"):
raise errors.AnsibleFileNotFound("%s is not a module" % module_name)
# Search module path(s) for named module.
in_path = utils.plugins.module_finder.find_plugin(module_name)
if in_path is None:
raise errors.AnsibleFileNotFound("module %s not found in %s" % (module_name, utils.plugins.module_finder.print_paths()))
out_path = os.path.join(tmp, module_name)
module_data = ""
is_new_style=False
with open(in_path) as f:
module_data = f.read()
if module_common.REPLACER in module_data:
is_new_style=True
module_data = module_data.replace(module_common.REPLACER, module_common.MODULE_COMMON)
encoded_args = "\"\"\"%s\"\"\"" % module_args.replace("\"","\\\"")
module_data = module_data.replace(module_common.REPLACER_ARGS, encoded_args)
encoded_lang = "\"\"\"%s\"\"\"" % C.DEFAULT_MODULE_LANG
module_data = module_data.replace(module_common.REPLACER_LANG, encoded_lang)
if is_new_style:
facility = C.DEFAULT_SYSLOG_FACILITY
if 'ansible_syslog_facility' in inject:
facility = inject['ansible_syslog_facility']
module_data = module_data.replace('syslog.LOG_USER', "syslog.%s" % facility)
lines = module_data.split("\n")
shebang = None
if lines[0].startswith("#!"):
shebang = lines[0]
args = shlex.split(str(shebang[2:]))
interpreter = args[0]
interpreter_config = 'ansible_%s_interpreter' % os.path.basename(interpreter)
if interpreter_config in inject:
lines[0] = shebang = "#!%s %s" % (inject[interpreter_config], " ".join(args[1:]))
module_data = "\n".join(lines)
self._transfer_str(conn, tmp, module_name, module_data)
return (out_path, is_new_style, shebang) | python | def _copy_module(self, conn, tmp, module_name, module_args, inject):
''' transfer a module over SFTP, does not run it '''
if module_name.startswith("/"):
raise errors.AnsibleFileNotFound("%s is not a module" % module_name)
# Search module path(s) for named module.
in_path = utils.plugins.module_finder.find_plugin(module_name)
if in_path is None:
raise errors.AnsibleFileNotFound("module %s not found in %s" % (module_name, utils.plugins.module_finder.print_paths()))
out_path = os.path.join(tmp, module_name)
module_data = ""
is_new_style=False
with open(in_path) as f:
module_data = f.read()
if module_common.REPLACER in module_data:
is_new_style=True
module_data = module_data.replace(module_common.REPLACER, module_common.MODULE_COMMON)
encoded_args = "\"\"\"%s\"\"\"" % module_args.replace("\"","\\\"")
module_data = module_data.replace(module_common.REPLACER_ARGS, encoded_args)
encoded_lang = "\"\"\"%s\"\"\"" % C.DEFAULT_MODULE_LANG
module_data = module_data.replace(module_common.REPLACER_LANG, encoded_lang)
if is_new_style:
facility = C.DEFAULT_SYSLOG_FACILITY
if 'ansible_syslog_facility' in inject:
facility = inject['ansible_syslog_facility']
module_data = module_data.replace('syslog.LOG_USER', "syslog.%s" % facility)
lines = module_data.split("\n")
shebang = None
if lines[0].startswith("#!"):
shebang = lines[0]
args = shlex.split(str(shebang[2:]))
interpreter = args[0]
interpreter_config = 'ansible_%s_interpreter' % os.path.basename(interpreter)
if interpreter_config in inject:
lines[0] = shebang = "#!%s %s" % (inject[interpreter_config], " ".join(args[1:]))
module_data = "\n".join(lines)
self._transfer_str(conn, tmp, module_name, module_data)
return (out_path, is_new_style, shebang) | [
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247,001 | cirruscluster/cirruscluster | cirruscluster/ext/ansible/runner/__init__.py | Runner._parallel_exec | def _parallel_exec(self, hosts):
''' handles mulitprocessing when more than 1 fork is required '''
if not hosts:
return
p = multiprocessing.Pool(self.forks)
results = []
#results = p.map(multiprocessing_runner, hosts) # can't handle keyboard interrupt
results = p.map_async(multiprocessing_runner, hosts).get(9999999)
p.close()
p.join()
return results | python | def _parallel_exec(self, hosts):
''' handles mulitprocessing when more than 1 fork is required '''
if not hosts:
return
p = multiprocessing.Pool(self.forks)
results = []
#results = p.map(multiprocessing_runner, hosts) # can't handle keyboard interrupt
results = p.map_async(multiprocessing_runner, hosts).get(9999999)
p.close()
p.join()
return results | [
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247,002 | cirruscluster/cirruscluster | cirruscluster/ext/ansible/runner/__init__.py | Runner._partition_results | def _partition_results(self, results):
''' seperate results by ones we contacted & ones we didn't '''
if results is None:
return None
results2 = dict(contacted={}, dark={})
for result in results:
host = result.host
if host is None:
raise Exception("internal error, host not set")
if result.communicated_ok():
results2["contacted"][host] = result.result
else:
results2["dark"][host] = result.result
# hosts which were contacted but never got a chance to return
for host in self.inventory.list_hosts(self.pattern):
if not (host in results2['dark'] or host in results2['contacted']):
results2["dark"][host] = {}
return results2 | python | def _partition_results(self, results):
''' seperate results by ones we contacted & ones we didn't '''
if results is None:
return None
results2 = dict(contacted={}, dark={})
for result in results:
host = result.host
if host is None:
raise Exception("internal error, host not set")
if result.communicated_ok():
results2["contacted"][host] = result.result
else:
results2["dark"][host] = result.result
# hosts which were contacted but never got a chance to return
for host in self.inventory.list_hosts(self.pattern):
if not (host in results2['dark'] or host in results2['contacted']):
results2["dark"][host] = {}
return results2 | [
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247,003 | cirruscluster/cirruscluster | cirruscluster/ext/ansible/runner/__init__.py | Runner.run | def run(self):
''' xfer & run module on all matched hosts '''
# find hosts that match the pattern
hosts = self.inventory.list_hosts(self.pattern)
if len(hosts) == 0:
self.callbacks.on_no_hosts()
return dict(contacted={}, dark={})
global multiprocessing_runner
multiprocessing_runner = self
results = None
# Check if this is an action plugin. Some of them are designed
# to be ran once per group of hosts. Example module: pause,
# run once per hostgroup, rather than pausing once per each
# host.
p = utils.plugins.action_loader.get(self.module_name, self)
if p and getattr(p, 'BYPASS_HOST_LOOP', None):
# Expose the current hostgroup to the bypassing plugins
self.host_set = hosts
# We aren't iterating over all the hosts in this
# group. So, just pick the first host in our group to
# construct the conn object with.
result_data = self._executor(hosts[0]).result
# Create a ResultData item for each host in this group
# using the returned result. If we didn't do this we would
# get false reports of dark hosts.
results = [ ReturnData(host=h, result=result_data, comm_ok=True) \
for h in hosts ]
del self.host_set
elif self.forks > 1:
try:
results = self._parallel_exec(hosts)
except IOError, ie:
print ie.errno
if ie.errno == 32:
# broken pipe from Ctrl+C
raise errors.AnsibleError("interupted")
raise
else:
results = [ self._executor(h) for h in hosts ]
return self._partition_results(results) | python | def run(self):
''' xfer & run module on all matched hosts '''
# find hosts that match the pattern
hosts = self.inventory.list_hosts(self.pattern)
if len(hosts) == 0:
self.callbacks.on_no_hosts()
return dict(contacted={}, dark={})
global multiprocessing_runner
multiprocessing_runner = self
results = None
# Check if this is an action plugin. Some of them are designed
# to be ran once per group of hosts. Example module: pause,
# run once per hostgroup, rather than pausing once per each
# host.
p = utils.plugins.action_loader.get(self.module_name, self)
if p and getattr(p, 'BYPASS_HOST_LOOP', None):
# Expose the current hostgroup to the bypassing plugins
self.host_set = hosts
# We aren't iterating over all the hosts in this
# group. So, just pick the first host in our group to
# construct the conn object with.
result_data = self._executor(hosts[0]).result
# Create a ResultData item for each host in this group
# using the returned result. If we didn't do this we would
# get false reports of dark hosts.
results = [ ReturnData(host=h, result=result_data, comm_ok=True) \
for h in hosts ]
del self.host_set
elif self.forks > 1:
try:
results = self._parallel_exec(hosts)
except IOError, ie:
print ie.errno
if ie.errno == 32:
# broken pipe from Ctrl+C
raise errors.AnsibleError("interupted")
raise
else:
results = [ self._executor(h) for h in hosts ]
return self._partition_results(results) | [
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247,004 | cirruscluster/cirruscluster | cirruscluster/ext/ansible/runner/__init__.py | Runner.run_async | def run_async(self, time_limit):
''' Run this module asynchronously and return a poller. '''
self.background = time_limit
results = self.run()
return results, poller.AsyncPoller(results, self) | python | def run_async(self, time_limit):
''' Run this module asynchronously and return a poller. '''
self.background = time_limit
results = self.run()
return results, poller.AsyncPoller(results, self) | [
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247,005 | kshlm/gant | gant/utils/docker_helper.py | DockerHelper.image_by_id | def image_by_id(self, id):
"""
Return image with given Id
"""
if not id:
return None
return next((image for image in self.images() if image['Id'] == id),
None) | python | def image_by_id(self, id):
"""
Return image with given Id
"""
if not id:
return None
return next((image for image in self.images() if image['Id'] == id),
None) | [
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247,006 | kshlm/gant | gant/utils/docker_helper.py | DockerHelper.image_by_tag | def image_by_tag(self, tag):
"""
Return image with given tag
"""
if not tag:
return None
return next((image for image in self.images() if tag
in image['RepoTags']), None) | python | def image_by_tag(self, tag):
"""
Return image with given tag
"""
if not tag:
return None
return next((image for image in self.images() if tag
in image['RepoTags']), None) | [
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247,007 | kshlm/gant | gant/utils/docker_helper.py | DockerHelper.image_exists | def image_exists(self, id=None, tag=None):
"""
Check if specified image exists
"""
exists = False
if id and self.image_by_id(id):
exists = True
elif tag and self.image_by_tag(tag):
exists = True
return exists | python | def image_exists(self, id=None, tag=None):
"""
Check if specified image exists
"""
exists = False
if id and self.image_by_id(id):
exists = True
elif tag and self.image_by_tag(tag):
exists = True
return exists | [
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247,008 | kshlm/gant | gant/utils/docker_helper.py | DockerHelper.container_by_id | def container_by_id(self, id):
"""
Returns container with given id
"""
if not id:
return None
return next((container for container in self.containers(all=True)
if container['Id'] == id), None) | python | def container_by_id(self, id):
"""
Returns container with given id
"""
if not id:
return None
return next((container for container in self.containers(all=True)
if container['Id'] == id), None) | [
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247,009 | kshlm/gant | gant/utils/docker_helper.py | DockerHelper.container_by_name | def container_by_name(self, name):
"""
Returns container with given name
"""
if not name:
return None
# docker prepends a '/' to container names in the container dict
name = '/'+name
return next((container for container in self.containers(all=True)
if name in container['Names']), None) | python | def container_by_name(self, name):
"""
Returns container with given name
"""
if not name:
return None
# docker prepends a '/' to container names in the container dict
name = '/'+name
return next((container for container in self.containers(all=True)
if name in container['Names']), None) | [
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247,010 | kshlm/gant | gant/utils/docker_helper.py | DockerHelper.container_exists | def container_exists(self, id=None, name=None):
"""
Checks if container exists already
"""
exists = False
if id and self.container_by_id(id):
exists = True
elif name and self.container_by_name(name):
exists = True
return exists | python | def container_exists(self, id=None, name=None):
"""
Checks if container exists already
"""
exists = False
if id and self.container_by_id(id):
exists = True
elif name and self.container_by_name(name):
exists = True
return exists | [
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247,011 | kshlm/gant | gant/utils/docker_helper.py | DockerHelper.container_running | def container_running(self, id=None, name=None):
"""
Checks if container is running
"""
running = False
if id:
running = self.inspect_container(id)['State']['Running']
elif name:
running = self.inspect_container(name)['State']['Running']
return running | python | def container_running(self, id=None, name=None):
"""
Checks if container is running
"""
running = False
if id:
running = self.inspect_container(id)['State']['Running']
elif name:
running = self.inspect_container(name)['State']['Running']
return running | [
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247,012 | kshlm/gant | gant/utils/docker_helper.py | DockerHelper.get_container_ip | def get_container_ip(self, container):
"""
Returns the internal ip of the container if available
"""
info = self.inspect_container(container)
if not info:
return None
netInfo = info['NetworkSettings']
if not netInfo:
return None
ip = netInfo['IPAddress']
if not ip:
return None
return ip | python | def get_container_ip(self, container):
"""
Returns the internal ip of the container if available
"""
info = self.inspect_container(container)
if not info:
return None
netInfo = info['NetworkSettings']
if not netInfo:
return None
ip = netInfo['IPAddress']
if not ip:
return None
return ip | [
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247,013 | polysquare/python-parse-shebang | parseshebang/__init__.py | _parse | def _parse(fileobj):
"""Parse fileobj for a shebang."""
fileobj.seek(0)
try:
part = fileobj.read(2)
except UnicodeDecodeError:
part = ""
if part == "#!":
shebang = shlex.split(fileobj.readline().strip())
if (platform.system() == "Windows" and
len(shebang) and
os.path.basename(shebang[0]) == "env"):
return shebang[1:]
return shebang
return [] | python | def _parse(fileobj):
"""Parse fileobj for a shebang."""
fileobj.seek(0)
try:
part = fileobj.read(2)
except UnicodeDecodeError:
part = ""
if part == "#!":
shebang = shlex.split(fileobj.readline().strip())
if (platform.system() == "Windows" and
len(shebang) and
os.path.basename(shebang[0]) == "env"):
return shebang[1:]
return shebang
return [] | [
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247,014 | tomokinakamaru/mapletree | mapletree/mapletree.py | MapleTree.run | def run(self, port=5000, background=False):
""" Runs this application with builtin server for testing.
This is only for test usage, do not use in production stage.
:param port: Port number
:param background: Flag to run in background
:type port: int
:type background: bool
"""
target = os.path.dirname(os.path.abspath(sys.argv[0]))
driver = Driver(self, port, target, 1)
if background:
driver.run_background()
else:
driver.run() | python | def run(self, port=5000, background=False):
""" Runs this application with builtin server for testing.
This is only for test usage, do not use in production stage.
:param port: Port number
:param background: Flag to run in background
:type port: int
:type background: bool
"""
target = os.path.dirname(os.path.abspath(sys.argv[0]))
driver = Driver(self, port, target, 1)
if background:
driver.run_background()
else:
driver.run() | [
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247,015 | stuaxo/mnd | mnd/dispatch.py | Dispatcher.unbind | def unbind(self, handler, argspec):
"""
handler will no longer be called if args match argspec
:param argspec: instance of ArgSpec - args to be matched
"""
self.handlers[argspec.key].remove((handler, argspec))
if not len(self.handlers[argspec.key]):
del self.handlers[argspec.key] | python | def unbind(self, handler, argspec):
"""
handler will no longer be called if args match argspec
:param argspec: instance of ArgSpec - args to be matched
"""
self.handlers[argspec.key].remove((handler, argspec))
if not len(self.handlers[argspec.key]):
del self.handlers[argspec.key] | [
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247,016 | stuaxo/mnd | mnd/dispatch.py | Dispatcher.dispatch | def dispatch(self, *args, **kwargs):
"""
Call handlers that match args or kwargs
:return: set of handlers called
"""
called_handlers = set()
for handler_list in self.handlers.values():
for handler, argspec in handler_list:
accept_args, accept_kwargs = argspec.accepts
if handler in called_handlers and False:
continue
else:
if args_match(accept_args, accept_kwargs, self.default, *args, **kwargs):
called_handlers.add(handler)
handler(*args, **kwargs)
return called_handlers | python | def dispatch(self, *args, **kwargs):
"""
Call handlers that match args or kwargs
:return: set of handlers called
"""
called_handlers = set()
for handler_list in self.handlers.values():
for handler, argspec in handler_list:
accept_args, accept_kwargs = argspec.accepts
if handler in called_handlers and False:
continue
else:
if args_match(accept_args, accept_kwargs, self.default, *args, **kwargs):
called_handlers.add(handler)
handler(*args, **kwargs)
return called_handlers | [
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247,017 | pbrisk/unicum | unicum/encode_json.py | UnicumJSONEncoder.iterencode | def iterencode(self, o, _one_shot=False):
"""Encode the given object and yield each string
representation as available.
For example::
for chunk in JSONEncoder().iterencode(bigobject):
mysocket.write(chunk)
"""
if self.check_circular:
markers = {}
else:
markers = None
if self.ensure_ascii:
_encoder = encode_basestring_ascii
else:
_encoder = encode_basestring
if self.encoding != 'utf-8':
def _encoder(o, _orig_encoder=_encoder, _encoding=self.encoding):
if isinstance(o, str):
o = o.decode(_encoding)
return _orig_encoder(o)
def floatstr(o, allow_nan=self.allow_nan,
_repr=FLOAT_REPR, _inf=INFINITY, _neginf=-INFINITY):
# Check for specials. Note that this type of test is processor
# and/or platform-specific, so do tests which don't depend on the
# internals.
if o != o:
text = 'NaN'
elif o == _inf:
text = 'Infinity'
elif o == _neginf:
text = '-Infinity'
else:
return _repr(o)
if not allow_nan:
raise ValueError(
"Out of range float values are not JSON compliant: " +
repr(o))
return text
_iterencode = _make_iterencode(
markers, self.default, _encoder, self.indent, floatstr,
self.key_separator, self.item_separator, self.sort_keys,
self.skipkeys, _one_shot, self._order)
return _iterencode(o, 0) | python | def iterencode(self, o, _one_shot=False):
"""Encode the given object and yield each string
representation as available.
For example::
for chunk in JSONEncoder().iterencode(bigobject):
mysocket.write(chunk)
"""
if self.check_circular:
markers = {}
else:
markers = None
if self.ensure_ascii:
_encoder = encode_basestring_ascii
else:
_encoder = encode_basestring
if self.encoding != 'utf-8':
def _encoder(o, _orig_encoder=_encoder, _encoding=self.encoding):
if isinstance(o, str):
o = o.decode(_encoding)
return _orig_encoder(o)
def floatstr(o, allow_nan=self.allow_nan,
_repr=FLOAT_REPR, _inf=INFINITY, _neginf=-INFINITY):
# Check for specials. Note that this type of test is processor
# and/or platform-specific, so do tests which don't depend on the
# internals.
if o != o:
text = 'NaN'
elif o == _inf:
text = 'Infinity'
elif o == _neginf:
text = '-Infinity'
else:
return _repr(o)
if not allow_nan:
raise ValueError(
"Out of range float values are not JSON compliant: " +
repr(o))
return text
_iterencode = _make_iterencode(
markers, self.default, _encoder, self.indent, floatstr,
self.key_separator, self.item_separator, self.sort_keys,
self.skipkeys, _one_shot, self._order)
return _iterencode(o, 0) | [
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247,018 | EventTeam/beliefs | src/beliefs/cells/lazy.py | LazyCell.update | def update(self):
"""
Updates intension and then adds or includes extension
"""
# updates intension
self.update_intension()
self._size_known_intension = len(self.members)
self._update_members = False | python | def update(self):
"""
Updates intension and then adds or includes extension
"""
# updates intension
self.update_intension()
self._size_known_intension = len(self.members)
self._update_members = False | [
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247,019 | EventTeam/beliefs | src/beliefs/cells/lazy.py | LazyCell.is_entailed_by | def is_entailed_by(self, other):
"""
Means merging other with self does not produce any new information.
"""
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if not self.exclude.isuperset(other.exclude):
return False
if not self.prototype.is_entailed_by(other.prototype):
return False
return True | python | def is_entailed_by(self, other):
"""
Means merging other with self does not produce any new information.
"""
if not set(self.include.keys()).issubset(set(other.include.keys())):
return False
if not self.exclude.isuperset(other.exclude):
return False
if not self.prototype.is_entailed_by(other.prototype):
return False
return True | [
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247,020 | EventTeam/beliefs | src/beliefs/cells/lazy.py | LazyCell.get_instances | def get_instances(self):
"""
Returns the members of the LazyDict
"""
if self._update_members: self.update()
return iter(sorted(self.members.iteritems())) | python | def get_instances(self):
"""
Returns the members of the LazyDict
"""
if self._update_members: self.update()
return iter(sorted(self.members.iteritems())) | [
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247,021 | chatfirst/chatfirst | chatfirst/client.py | Chatfirst.bots_list | def bots_list(self):
"""
List all user's bots
:rtype: list of Bot
:return: user's bots
"""
data = self.client.bots()
return [Bot(item) for item in data] | python | def bots_list(self):
"""
List all user's bots
:rtype: list of Bot
:return: user's bots
"""
data = self.client.bots()
return [Bot(item) for item in data] | [
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247,022 | chatfirst/chatfirst | chatfirst/client.py | Chatfirst.bots_create | def bots_create(self, bot):
"""
Save new bot
:param bot: bot object to save
:type bot: Bot
"""
self.client.bots(_method="POST", _json=bot.to_json(), _params=dict(userToken=self.token)) | python | def bots_create(self, bot):
"""
Save new bot
:param bot: bot object to save
:type bot: Bot
"""
self.client.bots(_method="POST", _json=bot.to_json(), _params=dict(userToken=self.token)) | [
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247,023 | chatfirst/chatfirst | chatfirst/client.py | Chatfirst.bots_get | def bots_get(self, bot):
"""
Fetch and fill Bot object
:param bot: empty bot object with name to search
:type bot: Bot
:rtype: Bot
:return: filled bot object
"""
data = self.client.bots.__getattr__(bot.name).__call__()
return Bot(data) | python | def bots_get(self, bot):
"""
Fetch and fill Bot object
:param bot: empty bot object with name to search
:type bot: Bot
:rtype: Bot
:return: filled bot object
"""
data = self.client.bots.__getattr__(bot.name).__call__()
return Bot(data) | [
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247,024 | chatfirst/chatfirst | chatfirst/client.py | Chatfirst.bots_delete | def bots_delete(self, bot):
"""
Delete existing bot
:param bot: bot to delete
:type bot: Bot
"""
self.client.bots.__getattr__(bot.name).__call__(_method="DELETE", _params=dict(botName=bot.name)) | python | def bots_delete(self, bot):
"""
Delete existing bot
:param bot: bot to delete
:type bot: Bot
"""
self.client.bots.__getattr__(bot.name).__call__(_method="DELETE", _params=dict(botName=bot.name)) | [
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247,025 | chatfirst/chatfirst | chatfirst/client.py | Chatfirst.talk | def talk(self, bot, message):
"""
Talk to bot and get response based
You can use this method to integrate the platform with your own channels
:param bot: bot to talk to
:type bot: Bot
:param message: message to send to bot
:type message: Message
:rtype: ActionResponse
:return: response object
"""
data = self.client.talk(_method="POST", _params=dict(botName=bot.name), _json=message.to_json())
return ActionResponse(data) | python | def talk(self, bot, message):
"""
Talk to bot and get response based
You can use this method to integrate the platform with your own channels
:param bot: bot to talk to
:type bot: Bot
:param message: message to send to bot
:type message: Message
:rtype: ActionResponse
:return: response object
"""
data = self.client.talk(_method="POST", _params=dict(botName=bot.name), _json=message.to_json())
return ActionResponse(data) | [
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247,026 | chatfirst/chatfirst | chatfirst/client.py | Chatfirst.push | def push(self, bot, channel_type, ar, user_id):
"""
Use this method to push message to user of bot.
The message should be packed into ActionResponse object.
This allows to push text messages, buttons, images.
This also allows to force current state of user.
:param bot: bot that will push user
:type bot: Bot
:param channel_type: one of [telegram, facebook, slack]
:type channel_type: str
:param ar: message packed in response object
:type ar: ActionResponse
:param user_id: user id in used channel
:type user_id: str
"""
self.client.push.__getattr__(bot.name).__call__(_method="POST",
_params=dict(id=user_id, channel=channel_type),
_json=ar.to_json()) | python | def push(self, bot, channel_type, ar, user_id):
"""
Use this method to push message to user of bot.
The message should be packed into ActionResponse object.
This allows to push text messages, buttons, images.
This also allows to force current state of user.
:param bot: bot that will push user
:type bot: Bot
:param channel_type: one of [telegram, facebook, slack]
:type channel_type: str
:param ar: message packed in response object
:type ar: ActionResponse
:param user_id: user id in used channel
:type user_id: str
"""
self.client.push.__getattr__(bot.name).__call__(_method="POST",
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_json=ar.to_json()) | [
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247,027 | chatfirst/chatfirst | chatfirst/client.py | Chatfirst.broadcast | def broadcast(self, bot, channel_type, text):
"""
Use this method to broadcast text message to all users of bot.
:param bot: bot that will push user
:type bot: Bot
:param channel_type: one of [telegram, facebook, slack]
:type channel_type: str
:param text: text message
:type text: str
"""
self.client.broadcast.__getattr__(bot.name).__call__(_method="POST",
_params=dict(channel=channel_type),
_json=dict(message=text)) | python | def broadcast(self, bot, channel_type, text):
"""
Use this method to broadcast text message to all users of bot.
:param bot: bot that will push user
:type bot: Bot
:param channel_type: one of [telegram, facebook, slack]
:type channel_type: str
:param text: text message
:type text: str
"""
self.client.broadcast.__getattr__(bot.name).__call__(_method="POST",
_params=dict(channel=channel_type),
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247,028 | luiscberrocal/pyjavaprops | pyjavaprops/javaproperties.py | JavaProperties.__parse | def __parse(self, lines):
""" Parse a list of lines and create
an internal property dictionary """
# Every line in the file must consist of either a comment
# or a key-value pair. A key-value pair is a line consisting
# of a key which is a combination of non-white space characters
# The separator character between key-value pairs is a '=',
# ':' or a whitespace character not including the newline.
# If the '=' or ':' characters are found, in the line, even
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# A line with only a key according to the rules above is also
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# In order to include characters '=' or ':' in a key or value,
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# Some examples of valid key-value pairs:
#
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# key=value
# key:value
# key value1,value2,value3
# key value1,value2,value3 \
# value4, value5
# key
# This key= this value
# key = value1 value2 value3
# Any line that starts with a '#' or '!' is considerered a comment
# and skipped. Also any trailing or preceding whitespaces
# are removed from the key/value.
# This is a line parser. It parses the
# contents like by line.
lineno=0
i = iter(lines)
for line in i:
lineno += 1
line = line.strip()
# Skip null lines
if not line: continue
# Skip lines which are comments
if line[0] in ('#','!'): continue
# Some flags
escaped=False
# Position of first separation char
sepidx = -1
# A flag for performing wspace re check
flag = 0
# Check for valid space separation
# First obtain the max index to which we
# can search.
m = self.othercharre.search(line)
if m:
first, last = m.span()
start, end = 0, first
flag = 1
wspacere = re.compile(r'(?<![\\\=\:])(\s)')
else:
if self.othercharre2.search(line):
# Check if either '=' or ':' is present
# in the line. If they are then it means
# they are preceded by a backslash.
# This means, we need to modify the
# wspacere a bit, not to look for
# : or = characters.
wspacere = re.compile(r'(?<![\\])(\s)')
start, end = 0, len(line)
m2 = wspacere.search(line, start, end)
if m2:
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# Means we need to split by space.
first, last = m2.span()
sepidx = first
elif m:
# print 'Other match=>',line
# No matching wspace char found, need
# to split by either '=' or ':'
first, last = m.span()
sepidx = last - 1
# print line[sepidx]
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# it has to be preceded by a space in which
# case the next line is read as part of the
# same property
while line[-1] == '\\':
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lineno += 1
# This line will become part of the value
line = line[:-1] + nextline
# Now split to key,value according to separation char
if sepidx != -1:
key, value = line[:sepidx], line[sepidx+1:]
else:
key,value = line,''
self._keyorder.append(key)
self.process_pair(key, value) | python | def __parse(self, lines):
""" Parse a list of lines and create
an internal property dictionary """
# Every line in the file must consist of either a comment
# or a key-value pair. A key-value pair is a line consisting
# of a key which is a combination of non-white space characters
# The separator character between key-value pairs is a '=',
# ':' or a whitespace character not including the newline.
# If the '=' or ':' characters are found, in the line, even
# keys containing whitespace chars are allowed.
# A line with only a key according to the rules above is also
# fine. In such case, the value is considered as the empty string.
# In order to include characters '=' or ':' in a key or value,
# they have to be properly escaped using the backslash character.
# Some examples of valid key-value pairs:
#
# key value
# key=value
# key:value
# key value1,value2,value3
# key value1,value2,value3 \
# value4, value5
# key
# This key= this value
# key = value1 value2 value3
# Any line that starts with a '#' or '!' is considerered a comment
# and skipped. Also any trailing or preceding whitespaces
# are removed from the key/value.
# This is a line parser. It parses the
# contents like by line.
lineno=0
i = iter(lines)
for line in i:
lineno += 1
line = line.strip()
# Skip null lines
if not line: continue
# Skip lines which are comments
if line[0] in ('#','!'): continue
# Some flags
escaped=False
# Position of first separation char
sepidx = -1
# A flag for performing wspace re check
flag = 0
# Check for valid space separation
# First obtain the max index to which we
# can search.
m = self.othercharre.search(line)
if m:
first, last = m.span()
start, end = 0, first
flag = 1
wspacere = re.compile(r'(?<![\\\=\:])(\s)')
else:
if self.othercharre2.search(line):
# Check if either '=' or ':' is present
# in the line. If they are then it means
# they are preceded by a backslash.
# This means, we need to modify the
# wspacere a bit, not to look for
# : or = characters.
wspacere = re.compile(r'(?<![\\])(\s)')
start, end = 0, len(line)
m2 = wspacere.search(line, start, end)
if m2:
# print 'Space match=>',line
# Means we need to split by space.
first, last = m2.span()
sepidx = first
elif m:
# print 'Other match=>',line
# No matching wspace char found, need
# to split by either '=' or ':'
first, last = m.span()
sepidx = last - 1
# print line[sepidx]
# If the last character is a backslash
# it has to be preceded by a space in which
# case the next line is read as part of the
# same property
while line[-1] == '\\':
# Read next line
nextline = next(i)
nextline = nextline.strip()
lineno += 1
# This line will become part of the value
line = line[:-1] + nextline
# Now split to key,value according to separation char
if sepidx != -1:
key, value = line[:sepidx], line[sepidx+1:]
else:
key,value = line,''
self._keyorder.append(key)
self.process_pair(key, value) | [
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247,029 | luiscberrocal/pyjavaprops | pyjavaprops/javaproperties.py | JavaProperties.load | def load(self, stream):
""" Load properties from an open file stream """
# For the time being only accept file input streams
if not _is_file(stream):
raise TypeError('Argument should be a file object!')
# Check for the opened mode
if stream.mode != 'r':
raise ValueError('Stream should be opened in read-only mode!')
try:
lines = stream.readlines()
self.__parse(lines)
except IOError:
raise | python | def load(self, stream):
""" Load properties from an open file stream """
# For the time being only accept file input streams
if not _is_file(stream):
raise TypeError('Argument should be a file object!')
# Check for the opened mode
if stream.mode != 'r':
raise ValueError('Stream should be opened in read-only mode!')
try:
lines = stream.readlines()
self.__parse(lines)
except IOError:
raise | [
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247,030 | luiscberrocal/pyjavaprops | pyjavaprops/javaproperties.py | JavaProperties.set_property | def set_property(self, key, value):
""" Set the property for the given key """
if type(key) is str and type(value) is str:
self.process_pair(key, value)
else:
raise TypeError('Both key and value should be strings!') | python | def set_property(self, key, value):
""" Set the property for the given key """
if type(key) is str and type(value) is str:
self.process_pair(key, value)
else:
raise TypeError('Both key and value should be strings!') | [
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247,031 | luiscberrocal/pyjavaprops | pyjavaprops/javaproperties.py | JavaProperties.list | def list(self, out=sys.stdout):
""" Prints a listing of the properties to the
stream 'out' which defaults to the standard output """
out.write('-- listing properties --\n')
for key,value in self._properties.items():
out.write(''.join((key,'=',value,'\n'))) | python | def list(self, out=sys.stdout):
""" Prints a listing of the properties to the
stream 'out' which defaults to the standard output """
out.write('-- listing properties --\n')
for key,value in self._properties.items():
out.write(''.join((key,'=',value,'\n'))) | [
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247,032 | luiscberrocal/pyjavaprops | pyjavaprops/javaproperties.py | JavaProperties.store | def store(self, out, header=""):
""" Write the properties list to the stream 'out' along
with the optional 'header' """
if out.mode[0] != 'w':
raise ValueError('Steam should be opened in write mode!')
try:
out.write(''.join(('#',header,'\n')))
# Write timestamp
tstamp = time.strftime('%a %b %d %H:%M:%S %Z %Y', time.localtime())
out.write(''.join(('#',tstamp,'\n')))
# Write properties from the pristine dictionary
for prop in self._keyorder:
if prop in self._origprops:
val = self._origprops[prop]
out.write(''.join((prop,'=',self.escape(val),'\n')))
out.close()
except IOError:
raise | python | def store(self, out, header=""):
""" Write the properties list to the stream 'out' along
with the optional 'header' """
if out.mode[0] != 'w':
raise ValueError('Steam should be opened in write mode!')
try:
out.write(''.join(('#',header,'\n')))
# Write timestamp
tstamp = time.strftime('%a %b %d %H:%M:%S %Z %Y', time.localtime())
out.write(''.join(('#',tstamp,'\n')))
# Write properties from the pristine dictionary
for prop in self._keyorder:
if prop in self._origprops:
val = self._origprops[prop]
out.write(''.join((prop,'=',self.escape(val),'\n')))
out.close()
except IOError:
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247,033 | swans-one/django-kittens | django_kittens/models.py | KittenManager.get_random | def get_random(self):
"""Get a kitten, either from the db, or a new one.
"""
num_kittens = self.count()
new_cutoff = (num_kittens / (num_kittens + constants.KITTEN_FRESHNESS))
if random.random() < new_cutoff:
return self._rand_inst()
else:
return self.create_new() | python | def get_random(self):
"""Get a kitten, either from the db, or a new one.
"""
num_kittens = self.count()
new_cutoff = (num_kittens / (num_kittens + constants.KITTEN_FRESHNESS))
if random.random() < new_cutoff:
return self._rand_inst()
else:
return self.create_new() | [
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247,034 | zaturox/glin | glin/__main__.py | boot | def boot():
"""Read configuration files, initialize glin and run main loop"""
argparser = argparse.ArgumentParser(
description="Controller for LED stripes (WS2801, WS2811 an similar)")
argparser.add_argument("-c", "--config", metavar="CONFIGFILE", dest="configfiles", action='append',
help='Configuration File. May be repeated multiple times. Later configuration files override previous ones.')
argparser.add_argument("-d", "--debug", dest="log_debug", action='store_const', const=True, help='Set log level to debug. Overrides -i/--info')
argparser.add_argument("-i", "--info", dest="log_info", action='store_const', const=True, help='Set log level to info.')
args = argparser.parse_args()
if args.log_debug:
logging.basicConfig(level=logging.DEBUG)
elif args.log_info:
logging.basicConfig(level=logging.INFO)
cfg = configparser.ConfigParser()
cfgpath = os.path.join(os.path.dirname(__file__), "default.conf")
cfg.read(cfgpath)
if args.configfiles is not None:
cfg.read(args.configfiles)
if "core" not in cfg:
logging.critical("No [core] section found in configurations files")
sys.exit()
if "leds" not in cfg["core"]:
logging.critical("No leds value found in [core] section in configurations files")
sys.exit()
led_count = int(cfg["core"]["leds"])
if "hwbackend" not in cfg["core"]:
logging.critical("No hwbackend value found in [core] section in configurations files")
sys.exit()
backend_name = cfg["core"]["hwbackend"]
hwbackends = list(iter_entry_points(group='glin.hwbackend', name=backend_name))
if len(hwbackends) != 1:
logging.critical("Found multiple hwbackend with same name. Cant decide upon one. Quitting.")
sys.exit()
backend_class = hwbackends[0].load()
backend_configuration = dict(cfg[backend_name]) if backend_name in cfg else {}
backend = backend_class(led_count=led_count, config=backend_configuration)
app = glin.app.GlinApp(led_count, hw_backend=backend)
for entry_point in iter_entry_points(group='glin.animation', name=None):
animation_class = entry_point.load()
try:
if issubclass(animation_class, glin.animations.AbstractAnimation):
app.register_animation(animation_class)
else:
logging.error("This is not a valid animation class. Has to be subclass of glin.animations:AbstraktAnimation. Ignoring.: {ep}"
.format(ep=entry_point))
except TypeError:
logging.error("This is not a Class. Ignoring.: {ep}".format(ep=entry_point))
app.execute() | python | def boot():
"""Read configuration files, initialize glin and run main loop"""
argparser = argparse.ArgumentParser(
description="Controller for LED stripes (WS2801, WS2811 an similar)")
argparser.add_argument("-c", "--config", metavar="CONFIGFILE", dest="configfiles", action='append',
help='Configuration File. May be repeated multiple times. Later configuration files override previous ones.')
argparser.add_argument("-d", "--debug", dest="log_debug", action='store_const', const=True, help='Set log level to debug. Overrides -i/--info')
argparser.add_argument("-i", "--info", dest="log_info", action='store_const', const=True, help='Set log level to info.')
args = argparser.parse_args()
if args.log_debug:
logging.basicConfig(level=logging.DEBUG)
elif args.log_info:
logging.basicConfig(level=logging.INFO)
cfg = configparser.ConfigParser()
cfgpath = os.path.join(os.path.dirname(__file__), "default.conf")
cfg.read(cfgpath)
if args.configfiles is not None:
cfg.read(args.configfiles)
if "core" not in cfg:
logging.critical("No [core] section found in configurations files")
sys.exit()
if "leds" not in cfg["core"]:
logging.critical("No leds value found in [core] section in configurations files")
sys.exit()
led_count = int(cfg["core"]["leds"])
if "hwbackend" not in cfg["core"]:
logging.critical("No hwbackend value found in [core] section in configurations files")
sys.exit()
backend_name = cfg["core"]["hwbackend"]
hwbackends = list(iter_entry_points(group='glin.hwbackend', name=backend_name))
if len(hwbackends) != 1:
logging.critical("Found multiple hwbackend with same name. Cant decide upon one. Quitting.")
sys.exit()
backend_class = hwbackends[0].load()
backend_configuration = dict(cfg[backend_name]) if backend_name in cfg else {}
backend = backend_class(led_count=led_count, config=backend_configuration)
app = glin.app.GlinApp(led_count, hw_backend=backend)
for entry_point in iter_entry_points(group='glin.animation', name=None):
animation_class = entry_point.load()
try:
if issubclass(animation_class, glin.animations.AbstractAnimation):
app.register_animation(animation_class)
else:
logging.error("This is not a valid animation class. Has to be subclass of glin.animations:AbstraktAnimation. Ignoring.: {ep}"
.format(ep=entry_point))
except TypeError:
logging.error("This is not a Class. Ignoring.: {ep}".format(ep=entry_point))
app.execute() | [
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247,035 | xtrementl/focus | focus/plugin/modules/sounds.py | PlaySound._play_sound | def _play_sound(self, filename):
""" Shells player with the provided filename.
`filename`
Filename for sound file.
"""
command = self._get_external_player()
if not command:
return # no player found
if common.IS_MACOSX:
command += ' "{0}"'.format(filename)
else:
# append quiet flag and filename
is_play = (command == 'play')
command += ' -q "{0}"'.format(filename)
# HACK: play can default to using pulseaudio. here, we
# check if pulse command exists and delegate to alsa if
# not
if is_play and not common.which('pulseaudio'):
command += ' -t alsa'
# play sound file, ignore if it fails
common.shell_process(command, background=True) | python | def _play_sound(self, filename):
""" Shells player with the provided filename.
`filename`
Filename for sound file.
"""
command = self._get_external_player()
if not command:
return # no player found
if common.IS_MACOSX:
command += ' "{0}"'.format(filename)
else:
# append quiet flag and filename
is_play = (command == 'play')
command += ' -q "{0}"'.format(filename)
# HACK: play can default to using pulseaudio. here, we
# check if pulse command exists and delegate to alsa if
# not
if is_play and not common.which('pulseaudio'):
command += ' -t alsa'
# play sound file, ignore if it fails
common.shell_process(command, background=True) | [
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247,036 | xtrementl/focus | focus/plugin/modules/sounds.py | PlaySound.parse_option | def parse_option(self, option, block_name, *values):
""" Parse options for play, end_play, and timer_play.
"""
if len(values) != 1:
raise TypeError
value = os.path.realpath(os.path.expanduser(values[0]))
if not os.path.isfile(value) and not os.path.islink(value):
raise ValueError(u'Sound file "{0}" does not exist'
.format(value))
# special extension check for aplay player
ext = os.path.splitext(value)[1].lower()
if ext != 'wav' and self._get_external_player() == 'aplay':
raise ValueError(u"Only WAV sound file "
"supported for 'aplay'")
if option == 'play':
option = 'start_' + option
key = option.split('_', 1)[0]
self.files[key] = value | python | def parse_option(self, option, block_name, *values):
""" Parse options for play, end_play, and timer_play.
"""
if len(values) != 1:
raise TypeError
value = os.path.realpath(os.path.expanduser(values[0]))
if not os.path.isfile(value) and not os.path.islink(value):
raise ValueError(u'Sound file "{0}" does not exist'
.format(value))
# special extension check for aplay player
ext = os.path.splitext(value)[1].lower()
if ext != 'wav' and self._get_external_player() == 'aplay':
raise ValueError(u"Only WAV sound file "
"supported for 'aplay'")
if option == 'play':
option = 'start_' + option
key = option.split('_', 1)[0]
self.files[key] = value | [
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247,037 | xtrementl/focus | focus/plugin/modules/sounds.py | PlaySound.on_taskend | def on_taskend(self, task):
""" Play sounds at task end.
"""
key = 'timer' if task.elapsed else 'end'
filename = self.files.get(key)
if filename:
self._play_sound(filename) | python | def on_taskend(self, task):
""" Play sounds at task end.
"""
key = 'timer' if task.elapsed else 'end'
filename = self.files.get(key)
if filename:
self._play_sound(filename) | [
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247,038 | brbsix/python-batchpath | batchpath.py | _fixpath | def _fixpath(root, base):
"""Return absolute, normalized, joined paths"""
return os.path.abspath(os.path.normpath(os.path.join(root, base))) | python | def _fixpath(root, base):
"""Return absolute, normalized, joined paths"""
return os.path.abspath(os.path.normpath(os.path.join(root, base))) | [
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247,039 | brbsix/python-batchpath | batchpath.py | _sorter | def _sorter(generated):
"""Return a list of paths sorted by dirname & basename."""
pairs = [(os.path.dirname(f), os.path.basename(f))
for f in set(list(generated))]
pairs.sort()
return [os.path.join(pair[0], pair[1]) for pair in pairs] | python | def _sorter(generated):
"""Return a list of paths sorted by dirname & basename."""
pairs = [(os.path.dirname(f), os.path.basename(f))
for f in set(list(generated))]
pairs.sort()
return [os.path.join(pair[0], pair[1]) for pair in pairs] | [
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247,040 | brbsix/python-batchpath | batchpath.py | _walk | def _walk(recursion):
"""Returns a recursive or non-recursive directory walker"""
try:
from scandir import walk as walk_function
except ImportError:
from os import walk as walk_function
if recursion:
walk = partial(walk_function)
else:
def walk(path): # pylint: disable=C0111
try:
yield next(walk_function(path))
except NameError:
yield walk_function(path)
return walk | python | def _walk(recursion):
"""Returns a recursive or non-recursive directory walker"""
try:
from scandir import walk as walk_function
except ImportError:
from os import walk as walk_function
if recursion:
walk = partial(walk_function)
else:
def walk(path): # pylint: disable=C0111
try:
yield next(walk_function(path))
except NameError:
yield walk_function(path)
return walk | [
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247,041 | brbsix/python-batchpath | batchpath.py | isvalid | def isvalid(path, access=None, extensions=None, filetype=None, minsize=None):
"""Check whether file meets access, extension, size, and type criteria."""
return ((access is None or os.access(path, access)) and
(extensions is None or checkext(path, extensions)) and
(((filetype == 'all' and os.path.exists(path)) or
(filetype == 'dir' and os.path.isdir(path)) or
(filetype == 'file' and os.path.isfile(path))) or
filetype is None) and
(minsize is None or (not os.path.isfile(path) or
os.path.getsize(path) > minsize))) | python | def isvalid(path, access=None, extensions=None, filetype=None, minsize=None):
"""Check whether file meets access, extension, size, and type criteria."""
return ((access is None or os.access(path, access)) and
(extensions is None or checkext(path, extensions)) and
(((filetype == 'all' and os.path.exists(path)) or
(filetype == 'dir' and os.path.isdir(path)) or
(filetype == 'file' and os.path.isfile(path))) or
filetype is None) and
(minsize is None or (not os.path.isfile(path) or
os.path.getsize(path) > minsize))) | [
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247,042 | brbsix/python-batchpath | batchpath.py | GeneratePaths._generator_file | def _generator_file(self):
"""Generator for `self.filetype` of 'file'"""
for path in self.paths:
if os.path.isfile(path):
if isvalid(path, self.access, self.extensions,
minsize=self.minsize):
yield os.path.abspath(path)
elif os.path.isdir(path):
for root, _, fnames in self._walker(path):
yield from self._generator_rebase(fnames, root) | python | def _generator_file(self):
"""Generator for `self.filetype` of 'file'"""
for path in self.paths:
if os.path.isfile(path):
if isvalid(path, self.access, self.extensions,
minsize=self.minsize):
yield os.path.abspath(path)
elif os.path.isdir(path):
for root, _, fnames in self._walker(path):
yield from self._generator_rebase(fnames, root) | [
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247,043 | brbsix/python-batchpath | batchpath.py | GeneratePaths._generator_other | def _generator_other(self):
"""Generator for `self.filetype` other than file"""
for path in self.paths:
for root, dnames, fnames in self._walker(path):
yield from self._generator_rebase(dnames, root)
yield from self._generator_rebase(fnames, root) | python | def _generator_other(self):
"""Generator for `self.filetype` other than file"""
for path in self.paths:
for root, dnames, fnames in self._walker(path):
yield from self._generator_rebase(dnames, root)
yield from self._generator_rebase(fnames, root) | [
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247,044 | brbsix/python-batchpath | batchpath.py | VerifyPaths.all | def all(self, paths, access=None):
"""Verify list of paths"""
self.failures = [path for path in paths if not
isvalid(path, access, filetype='all')]
return not self.failures | python | def all(self, paths, access=None):
"""Verify list of paths"""
self.failures = [path for path in paths if not
isvalid(path, access, filetype='all')]
return not self.failures | [
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247,045 | brbsix/python-batchpath | batchpath.py | VerifyPaths.dirs | def dirs(self, paths, access=None):
"""Verify list of directories"""
self.failures = [path for path in paths if not
isvalid(path, access, filetype='dir')]
return not self.failures | python | def dirs(self, paths, access=None):
"""Verify list of directories"""
self.failures = [path for path in paths if not
isvalid(path, access, filetype='dir')]
return not self.failures | [
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247,046 | brbsix/python-batchpath | batchpath.py | VerifyPaths.files | def files(self, paths, access=None, extensions=None, minsize=None):
"""Verify list of files"""
self.failures = [path for path in paths if not
isvalid(path, access, extensions, 'file', minsize)]
return not self.failures | python | def files(self, paths, access=None, extensions=None, minsize=None):
"""Verify list of files"""
self.failures = [path for path in paths if not
isvalid(path, access, extensions, 'file', minsize)]
return not self.failures | [
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247,047 | dr4ke616/pinky | pinky/core/manhole.py | get_manhole_factory | def get_manhole_factory(namespace, **passwords):
"""Get a Manhole Factory
"""
realm = manhole_ssh.TerminalRealm()
realm.chainedProtocolFactory.protocolFactory = (
lambda _: EnhancedColoredManhole(namespace)
)
p = portal.Portal(realm)
p.registerChecker(
checkers.InMemoryUsernamePasswordDatabaseDontUse(**passwords)
)
return manhole_ssh.ConchFactory(p) | python | def get_manhole_factory(namespace, **passwords):
"""Get a Manhole Factory
"""
realm = manhole_ssh.TerminalRealm()
realm.chainedProtocolFactory.protocolFactory = (
lambda _: EnhancedColoredManhole(namespace)
)
p = portal.Portal(realm)
p.registerChecker(
checkers.InMemoryUsernamePasswordDatabaseDontUse(**passwords)
)
return manhole_ssh.ConchFactory(p) | [
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247,048 | chromy/essence | src/essence/world.py | World.create_entity | def create_entity(self):
"""Create a new entity.
The entity will have a higher UID than any previously associated
with this world.
:return: the new entity
:rtype: :class:`essence.Entity`"""
self._highest_id_seen += 1
entity = Entity(self._highest_id_seen, self)
self._entities.append(entity)
return entity | python | def create_entity(self):
"""Create a new entity.
The entity will have a higher UID than any previously associated
with this world.
:return: the new entity
:rtype: :class:`essence.Entity`"""
self._highest_id_seen += 1
entity = Entity(self._highest_id_seen, self)
self._entities.append(entity)
return entity | [
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247,049 | chromy/essence | src/essence/world.py | World.destroy_entitiy | def destroy_entitiy(self, entity):
"""Remove the entity and all connected components from the world.
Long-hand for :func:`essence.Entity.destroy`.
"""
for relation in self._database.values():
relation.pop(entity, None)
for l in self._entities_by_component.values():
l.discard(entity)
self._entities.remove(entity) | python | def destroy_entitiy(self, entity):
"""Remove the entity and all connected components from the world.
Long-hand for :func:`essence.Entity.destroy`.
"""
for relation in self._database.values():
relation.pop(entity, None)
for l in self._entities_by_component.values():
l.discard(entity)
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247,050 | chromy/essence | src/essence/world.py | World.add_component | def add_component(self, entity, component):
"""Add component to entity.
Long-hand for :func:`essence.Entity.add`.
:param entity: entity to associate
:type entity: :class:`essence.Entity`
:param component: component to add to the entity
:type component: :class:`essence.Component`"""
component_type = type(component)
relation = self._get_relation(component_type)
if entity in relation:
# PYTHON2.6: Numbers required in format string.
msg = "Component {0} can't be added to entity {1} since it already has a component of type {2}.".format(component, entity, component_type)
raise DuplicateComponentError(msg)
relation[entity] = component
self._entities_with(component_type).add(entity) | python | def add_component(self, entity, component):
"""Add component to entity.
Long-hand for :func:`essence.Entity.add`.
:param entity: entity to associate
:type entity: :class:`essence.Entity`
:param component: component to add to the entity
:type component: :class:`essence.Component`"""
component_type = type(component)
relation = self._get_relation(component_type)
if entity in relation:
# PYTHON2.6: Numbers required in format string.
msg = "Component {0} can't be added to entity {1} since it already has a component of type {2}.".format(component, entity, component_type)
raise DuplicateComponentError(msg)
relation[entity] = component
self._entities_with(component_type).add(entity) | [
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247,051 | chromy/essence | src/essence/world.py | World.get_component | def get_component(self, entity, component_type, missing=MISSING):
"""Get the component of type component_type associated with entity.
Long-hand for :func:`essence.Entity.get`.
:param entity: entity to query
:type entity: :class:`essence.Entity`
:param component_type: component to add to the entity
:type component_type: The :class:`type` of a :class:`Component` subclass
:param missing: value to return if
:type missing: :class:`essence.Component`
:raises:"""
relation = self._get_relation(component_type)
if entity not in relation:
if missing is MISSING:
raise NoSuchComponentError()
else:
return missing
return relation[entity] | python | def get_component(self, entity, component_type, missing=MISSING):
"""Get the component of type component_type associated with entity.
Long-hand for :func:`essence.Entity.get`.
:param entity: entity to query
:type entity: :class:`essence.Entity`
:param component_type: component to add to the entity
:type component_type: The :class:`type` of a :class:`Component` subclass
:param missing: value to return if
:type missing: :class:`essence.Component`
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relation = self._get_relation(component_type)
if entity not in relation:
if missing is MISSING:
raise NoSuchComponentError()
else:
return missing
return relation[entity] | [
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247,052 | chromy/essence | src/essence/world.py | World.remove_component | def remove_component(self, entity, component_type):
"""Remove the component of component_type from entity.
Long-hand for :func:`essence.Entity.remove`.
:param entity: entity to associate
:type entity: :class:`essence.Entity`
:param component_type: Type of component
:type component_type: The :class:`type` of a :class:`Component` subclass"""
relation = self._get_relation(component_type)
del relation[entity]
self._entities_with(component_type).remove(entity) | python | def remove_component(self, entity, component_type):
"""Remove the component of component_type from entity.
Long-hand for :func:`essence.Entity.remove`.
:param entity: entity to associate
:type entity: :class:`essence.Entity`
:param component_type: Type of component
:type component_type: The :class:`type` of a :class:`Component` subclass"""
relation = self._get_relation(component_type)
del relation[entity]
self._entities_with(component_type).remove(entity) | [
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] | 6cd18821ec91edf022619d9f0c0878f38c22a763 | https://github.com/chromy/essence/blob/6cd18821ec91edf022619d9f0c0878f38c22a763/src/essence/world.py#L94-L105 |
247,053 | chromy/essence | src/essence/world.py | World.update | def update(self, *args, **kwargs):
"""Calls update on each of the systems self.systems."""
for system in self.systems:
system.update(self, *args, **kwargs) | python | def update(self, *args, **kwargs):
"""Calls update on each of the systems self.systems."""
for system in self.systems:
system.update(self, *args, **kwargs) | [
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247,054 | djangomini/djangomini | djangomini/urls.py | auto_discover | def auto_discover():
"""
Auto-map urls from controllers directory.
Ignored only files and classes that start from underscore.
"""
urls = [
url(r'^admin/', admin.site.urls),
]
# TODO: we can create python package to have a lot of controllers
# in separate files
def get_controllers(module_name):
"""Return list of controllers in a module."""
module = import_module('app.controllers.{}'.format(module_name))
controllers = []
for obj_name in dir(module):
# we ignore import of Controller and hidden names
if obj_name.startswith('_') or obj_name == 'Controller':
continue
obj = getattr(module, obj_name)
# include only controllers
if issubclass(obj, Controller):
controllers.append(obj)
return controllers
def controller_to_path(controller):
"""
Convert controller's name to a valid path.
Make url in lower case by replace capital letters to small
and adding underscore between words.
"""
words = re.findall('[A-Z][a-z]*', controller.__name__)
if words[-1] == 'Controller':
del words[-1]
# transform words to a url address
url_path = '_'.join(words).lower()
# main controller is a root handler
# TODO: root address inside the file should always come last
if url_path == 'main':
url_path = ''
return url_path
# load all controllers (excluding main controllers)
for file_name in listdir('controllers', get_files=True, hide_ignored=True):
# remove .py extension from file name
app_name = file_name.split('.', 1)[0]
# we will include main controller at the end
if app_name == 'main':
continue
# add url for each controller
for controller in get_controllers(app_name):
url_path = controller_to_path(controller)
urls.append(url(
r'^{}/{}$'.format(app_name, url_path),
controller.as_view()
))
# add urls for main controllers
for controller in get_controllers('main'):
url_path = controller_to_path(controller)
# map urls to a root path
urls.append(url(
r'^{}$'.format(url_path),
controller.as_view()
))
return urls | python | def auto_discover():
"""
Auto-map urls from controllers directory.
Ignored only files and classes that start from underscore.
"""
urls = [
url(r'^admin/', admin.site.urls),
]
# TODO: we can create python package to have a lot of controllers
# in separate files
def get_controllers(module_name):
"""Return list of controllers in a module."""
module = import_module('app.controllers.{}'.format(module_name))
controllers = []
for obj_name in dir(module):
# we ignore import of Controller and hidden names
if obj_name.startswith('_') or obj_name == 'Controller':
continue
obj = getattr(module, obj_name)
# include only controllers
if issubclass(obj, Controller):
controllers.append(obj)
return controllers
def controller_to_path(controller):
"""
Convert controller's name to a valid path.
Make url in lower case by replace capital letters to small
and adding underscore between words.
"""
words = re.findall('[A-Z][a-z]*', controller.__name__)
if words[-1] == 'Controller':
del words[-1]
# transform words to a url address
url_path = '_'.join(words).lower()
# main controller is a root handler
# TODO: root address inside the file should always come last
if url_path == 'main':
url_path = ''
return url_path
# load all controllers (excluding main controllers)
for file_name in listdir('controllers', get_files=True, hide_ignored=True):
# remove .py extension from file name
app_name = file_name.split('.', 1)[0]
# we will include main controller at the end
if app_name == 'main':
continue
# add url for each controller
for controller in get_controllers(app_name):
url_path = controller_to_path(controller)
urls.append(url(
r'^{}/{}$'.format(app_name, url_path),
controller.as_view()
))
# add urls for main controllers
for controller in get_controllers('main'):
url_path = controller_to_path(controller)
# map urls to a root path
urls.append(url(
r'^{}$'.format(url_path),
controller.as_view()
))
return urls | [
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247,055 | heikomuller/sco-client | scocli/scoserv.py | download_file | def download_file(url, suffix=''):
"""Download attached file as temporary file.
Parameters
----------
url : string
SCO-API download Url
suffix : string, optional
If suffix is specified, the name of the downloaded file will end with
that suffix, otherwise there will be no suffix.
Returns
-------
string, string
Path to downloaded file and file suffix
"""
r = urllib2.urlopen(url)
# Save attached file in temp file and return path to temp file
fd, f_path = tempfile.mkstemp(suffix=suffix)
os.write(fd, r.read())
os.close(fd)
return f_path, suffix | python | def download_file(url, suffix=''):
"""Download attached file as temporary file.
Parameters
----------
url : string
SCO-API download Url
suffix : string, optional
If suffix is specified, the name of the downloaded file will end with
that suffix, otherwise there will be no suffix.
Returns
-------
string, string
Path to downloaded file and file suffix
"""
r = urllib2.urlopen(url)
# Save attached file in temp file and return path to temp file
fd, f_path = tempfile.mkstemp(suffix=suffix)
os.write(fd, r.read())
os.close(fd)
return f_path, suffix | [
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247,056 | heikomuller/sco-client | scocli/scoserv.py | get_resource_listing | def get_resource_listing(url, offset, limit, properties):
"""Gneric method to retrieve a resource listing from a SCO-API. Takes the
resource-specific API listing Url as argument.
Parameters
----------
url : string
Resource listing Url for a SCO-API
offset : int, optional
Starting offset for returned list items
limit : int, optional
Limit the number of items in the result
properties : List(string)
List of additional object properties to be included for items in
the result
Returns
-------
List(ResourceHandle)
List of resource handle (one per subject in the object listing)
"""
# Create listing query based on given arguments
query = [
QPARA_OFFSET + '=' + str(offset),
QPARA_LIMIT + '=' + str(limit)
]
# Add properties argument if property list is not None and not empty
if not properties is None:
if len(properties) > 0:
query.append(QPARA_ATTRIBUTES + '=' + ','.join(properties))
# Add query to Url.
url = url + '?' + '&'.join(query)
# Get subject listing Url for given SCO-API and decorate it with
# given listing arguments. Then retrieve listing from SCO-API.
json_obj = JsonResource(url).json
# Convert result into a list of resource handles and return the result
resources = []
for element in json_obj['items']:
resource = ResourceHandle(element)
# Add additional properties to resource if list is given
if not properties is None:
resource.properties = {}
for prop in properties:
if prop in element:
resource.properties[prop] = element[prop]
resources.append(resource)
return resources | python | def get_resource_listing(url, offset, limit, properties):
"""Gneric method to retrieve a resource listing from a SCO-API. Takes the
resource-specific API listing Url as argument.
Parameters
----------
url : string
Resource listing Url for a SCO-API
offset : int, optional
Starting offset for returned list items
limit : int, optional
Limit the number of items in the result
properties : List(string)
List of additional object properties to be included for items in
the result
Returns
-------
List(ResourceHandle)
List of resource handle (one per subject in the object listing)
"""
# Create listing query based on given arguments
query = [
QPARA_OFFSET + '=' + str(offset),
QPARA_LIMIT + '=' + str(limit)
]
# Add properties argument if property list is not None and not empty
if not properties is None:
if len(properties) > 0:
query.append(QPARA_ATTRIBUTES + '=' + ','.join(properties))
# Add query to Url.
url = url + '?' + '&'.join(query)
# Get subject listing Url for given SCO-API and decorate it with
# given listing arguments. Then retrieve listing from SCO-API.
json_obj = JsonResource(url).json
# Convert result into a list of resource handles and return the result
resources = []
for element in json_obj['items']:
resource = ResourceHandle(element)
# Add additional properties to resource if list is given
if not properties is None:
resource.properties = {}
for prop in properties:
if prop in element:
resource.properties[prop] = element[prop]
resources.append(resource)
return resources | [
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Resource listing Url for a SCO-API
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Limit the number of items in the result
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247,057 | heikomuller/sco-client | scocli/scoserv.py | to_local_time | def to_local_time(timestamp):
"""Convert a datatime object from UTC time to local time.
Adopted from:
http://stackoverflow.com/questions/4770297/python-convert-utc-datetime-string-to-local-datetime
Parameters
----------
timestamp : string
Default string representation of timestamps expected to be in
UTC time zone
Returns
-------
datetime
Datetime object in local time zone
"""
utc = dt.datetime.strptime(timestamp, '%Y-%m-%dT%H:%M:%S.%f')
# Get UTC and local time zone
from_zone = tz.gettz('UTC')
to_zone = tz.tzlocal()
# Tell the utc object that it is in UTC time zone
utc = utc.replace(tzinfo=from_zone)
# Convert time zone
return utc.astimezone(to_zone) | python | def to_local_time(timestamp):
"""Convert a datatime object from UTC time to local time.
Adopted from:
http://stackoverflow.com/questions/4770297/python-convert-utc-datetime-string-to-local-datetime
Parameters
----------
timestamp : string
Default string representation of timestamps expected to be in
UTC time zone
Returns
-------
datetime
Datetime object in local time zone
"""
utc = dt.datetime.strptime(timestamp, '%Y-%m-%dT%H:%M:%S.%f')
# Get UTC and local time zone
from_zone = tz.gettz('UTC')
to_zone = tz.tzlocal()
# Tell the utc object that it is in UTC time zone
utc = utc.replace(tzinfo=from_zone)
# Convert time zone
return utc.astimezone(to_zone) | [
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Default string representation of timestamps expected to be in
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247,058 | Clarify/clarify_brightcove_sync | clarify_brightcove_sync/brightcove_api_client.py | BrightcoveAPIClient._load_secret | def _load_secret(self, creds_file):
'''read the oauth secrets and account ID from a credentials configuration file'''
try:
with open(creds_file) as fp:
creds = json.load(fp)
return creds
except Exception as e:
sys.stderr.write("Error loading oauth secret from local file called '{0}'\n".format(creds_file))
sys.stderr.write("\tThere should be a local OAuth credentials file \n")
sys.stderr.write("\twhich has contents like this:\n")
sys.stderr.write("""
{
"account_id": "1234567890001",
"client_id": "30ff0909-0909-33d3-ae88-c9887777a7b7",
"client_secret": "mzKKjZZyeW5YgsdfBD37c5730g397agU35-Dsgeox6-73giehbt0996nQ"
}
""")
sys.stderr.write("\n")
raise e | python | def _load_secret(self, creds_file):
'''read the oauth secrets and account ID from a credentials configuration file'''
try:
with open(creds_file) as fp:
creds = json.load(fp)
return creds
except Exception as e:
sys.stderr.write("Error loading oauth secret from local file called '{0}'\n".format(creds_file))
sys.stderr.write("\tThere should be a local OAuth credentials file \n")
sys.stderr.write("\twhich has contents like this:\n")
sys.stderr.write("""
{
"account_id": "1234567890001",
"client_id": "30ff0909-0909-33d3-ae88-c9887777a7b7",
"client_secret": "mzKKjZZyeW5YgsdfBD37c5730g397agU35-Dsgeox6-73giehbt0996nQ"
}
""")
sys.stderr.write("\n")
raise e | [
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247,059 | Clarify/clarify_brightcove_sync | clarify_brightcove_sync/brightcove_api_client.py | BrightcoveAPIClient.get_video_count | def get_video_count(self, search_q=None):
'''Return the number of videos in the account'''
if search_q is not None:
params = {'q': search_q}
else:
params = None
url = "/counts/videos"
result = self._make_request(self.CMS_Server, 'GET', url, params=params)
return result['count'] | python | def get_video_count(self, search_q=None):
'''Return the number of videos in the account'''
if search_q is not None:
params = {'q': search_q}
else:
params = None
url = "/counts/videos"
result = self._make_request(self.CMS_Server, 'GET', url, params=params)
return result['count'] | [
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247,060 | Clarify/clarify_brightcove_sync | clarify_brightcove_sync/brightcove_api_client.py | BrightcoveAPIClient.post_video | def post_video(self, videoUrl, name=None, ingestMedia=True):
'''Post and optionally ingest media from the specified URL'''
if name is None:
name = os.path.basename(videoUrl)
url = '/videos'
data = {'name': name}
new_video = self._make_request(self.CMS_Server, 'POST', url, data=data)
if ingestMedia:
self.ingest_video(new_video['id'], videoUrl)
return new_video | python | def post_video(self, videoUrl, name=None, ingestMedia=True):
'''Post and optionally ingest media from the specified URL'''
if name is None:
name = os.path.basename(videoUrl)
url = '/videos'
data = {'name': name}
new_video = self._make_request(self.CMS_Server, 'POST', url, data=data)
if ingestMedia:
self.ingest_video(new_video['id'], videoUrl)
return new_video | [
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247,061 | cbrand/vpnchooser | src/vpnchooser/connection/client.py | Client.connect | def connect(self):
"""
Connects the client to the server and
returns it.
"""
key = paramiko.RSAKey(data=base64.b64decode(
app.config['SSH_HOST_KEY']
))
client = paramiko.SSHClient()
client.get_host_keys().add(
app.config['SSH_HOST'],
'ssh-rsa',
key
)
client.connect(
app.config['SSH_HOST'],
username=app.config['SSH_USER'],
password=app.config['SSH_PASSWORD'],
)
return client | python | def connect(self):
"""
Connects the client to the server and
returns it.
"""
key = paramiko.RSAKey(data=base64.b64decode(
app.config['SSH_HOST_KEY']
))
client = paramiko.SSHClient()
client.get_host_keys().add(
app.config['SSH_HOST'],
'ssh-rsa',
key
)
client.connect(
app.config['SSH_HOST'],
username=app.config['SSH_USER'],
password=app.config['SSH_PASSWORD'],
)
return client | [
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247,062 | cbrand/vpnchooser | src/vpnchooser/connection/client.py | Client.server_rules | def server_rules(self):
"""
Reads the server rules from the client
and returns it.
"""
sftp = self.client.open_sftp()
try:
rule_path = self.rule_location
try:
stat_entry = sftp.stat(rule_path)
if stat.S_ISDIR(stat_entry.st_mode):
sftp.rmdir(rule_path)
return []
except IOError:
return []
with sftp.open(rule_path, 'r') as file_handle:
data = file_handle.read()
return self._parse(data)
finally:
sftp.close() | python | def server_rules(self):
"""
Reads the server rules from the client
and returns it.
"""
sftp = self.client.open_sftp()
try:
rule_path = self.rule_location
try:
stat_entry = sftp.stat(rule_path)
if stat.S_ISDIR(stat_entry.st_mode):
sftp.rmdir(rule_path)
return []
except IOError:
return []
with sftp.open(rule_path, 'r') as file_handle:
data = file_handle.read()
return self._parse(data)
finally:
sftp.close() | [
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247,063 | cbrand/vpnchooser | src/vpnchooser/connection/client.py | Client._parse | def _parse(data: str) -> list:
"""
Parses the given data string and returns
a list of rule objects.
"""
if isinstance(data, bytes):
data = data.decode('utf-8')
lines = (
item for item in
(item.strip() for item in data.split('\n'))
if len(item) and not item.startswith('#')
)
rules = []
for line in lines:
rules.append(
Rule.parse(line)
)
return rules | python | def _parse(data: str) -> list:
"""
Parses the given data string and returns
a list of rule objects.
"""
if isinstance(data, bytes):
data = data.decode('utf-8')
lines = (
item for item in
(item.strip() for item in data.split('\n'))
if len(item) and not item.startswith('#')
)
rules = []
for line in lines:
rules.append(
Rule.parse(line)
)
return rules | [
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247,064 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | jaccardIndex | def jaccardIndex(s1, s2, stranded=False):
"""
Compute the Jaccard index for two collections of genomic intervals
:param s1: the first set of genomic intervals
:param s2: the second set of genomic intervals
:param stranded: if True, treat regions on different strands as not
intersecting each other, even if they occupy the same
genomic region.
:return: Jaccard index
"""
def count(s):
""" sum the size of regions in s. """
tot = 0
for r in s:
tot += len(r)
return tot
if stranded:
raise GenomicIntervalError("Sorry, stranded mode for computing Jaccard " +
"index hasn't been implemented yet.")
s1 = collapseRegions(s1)
s2 = collapseRegions(s2)
intersection = regionsIntersection(s1, s2)
c_i = count(intersection)
return c_i / float(count(s1) + count(s2) - c_i) | python | def jaccardIndex(s1, s2, stranded=False):
"""
Compute the Jaccard index for two collections of genomic intervals
:param s1: the first set of genomic intervals
:param s2: the second set of genomic intervals
:param stranded: if True, treat regions on different strands as not
intersecting each other, even if they occupy the same
genomic region.
:return: Jaccard index
"""
def count(s):
""" sum the size of regions in s. """
tot = 0
for r in s:
tot += len(r)
return tot
if stranded:
raise GenomicIntervalError("Sorry, stranded mode for computing Jaccard " +
"index hasn't been implemented yet.")
s1 = collapseRegions(s1)
s2 = collapseRegions(s2)
intersection = regionsIntersection(s1, s2)
c_i = count(intersection)
return c_i / float(count(s1) + count(s2) - c_i) | [
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247,065 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | intervalTreesFromList | def intervalTreesFromList(inElements, verbose=False, openEnded=False):
"""
build a dictionary, indexed by chrom name, of interval trees for each chrom.
:param inElements: list of genomic intervals. Members of the list must have
chrom, start and end fields; no other restrictions.
:param verbose: output progress messages to sys.stderr if True
"""
elements = {}
if verbose:
totalLines = len(inElements)
pind = ProgressIndicator(totalToDo=totalLines,
messagePrefix="completed",
messageSuffix="of parsing")
for element in inElements:
if element.chrom not in elements:
elements[element.chrom] = []
elements[element.chrom].append(element)
if verbose:
pind.done += 1
pind.showProgress()
# create an interval tree for each list
trees = {}
if verbose:
totalLines = len(elements)
pind = ProgressIndicator(totalToDo=totalLines,
messagePrefix="completed",
messageSuffix="of making interval trees")
for chrom in elements:
trees[chrom] = IntervalTree(elements[chrom], openEnded)
if verbose:
pind.done += 1
pind.showProgress()
return trees | python | def intervalTreesFromList(inElements, verbose=False, openEnded=False):
"""
build a dictionary, indexed by chrom name, of interval trees for each chrom.
:param inElements: list of genomic intervals. Members of the list must have
chrom, start and end fields; no other restrictions.
:param verbose: output progress messages to sys.stderr if True
"""
elements = {}
if verbose:
totalLines = len(inElements)
pind = ProgressIndicator(totalToDo=totalLines,
messagePrefix="completed",
messageSuffix="of parsing")
for element in inElements:
if element.chrom not in elements:
elements[element.chrom] = []
elements[element.chrom].append(element)
if verbose:
pind.done += 1
pind.showProgress()
# create an interval tree for each list
trees = {}
if verbose:
totalLines = len(elements)
pind = ProgressIndicator(totalToDo=totalLines,
messagePrefix="completed",
messageSuffix="of making interval trees")
for chrom in elements:
trees[chrom] = IntervalTree(elements[chrom], openEnded)
if verbose:
pind.done += 1
pind.showProgress()
return trees | [
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247,066 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | regionsIntersection | def regionsIntersection(s1, s2, collapse=True):
"""
given two lists of genomic regions with chromosome, start and end
coordinates, return a new list of regions which is the intersection of those
two sets. Lists must be sorted by chromosome and start index
:return: new list that represents the intersection of the two input lists.
output regions will all have name "X", be on strand "+" and have
score 0
:param s1: first list of genomic regions
:param s2: second list of genomic regions
:raise GenomicIntervalError: if the input regions are not sorted correctly
(by chromosome and start index)
:note: O(n) time, O(n) space; informally, might use up to 3x space of input
"""
debug = False
# we don't need to explicitly check for sorting because sorted order is
# a post-condition of the collapsing function
s1_c = collapseRegions(s1)
s2_c = collapseRegions(s2)
if len(s1_c) == 0 or len(s2_c) == 0:
return []
res = []
j = 0
for i in range(0, len(s1_c)):
if debug:
sys.stderr.write("processing from s1_c : " + str(s1_c[i]) + "\n")
# find first thing in s2_c with end in or after s1_c[i]
if debug:
sys.stderr.write("i = " + str(i) + " and j = " + str(j) + "\n")
while (j < len(s2_c) and
(s2_c[j].chrom < s1_c[i].chrom or
(s2_c[j].chrom == s1_c[i].chrom and s2_c[j].end <= s1_c[i].start))):
j += 1
# nothing intersects if we hit the end of s2, or the end of the chrom,
# or we're still on the same chrom but start after the end of s2_c[i]
if j >= len(s2_c) or s2_c[j].chrom > s1_c[i].chrom or \
(s2_c[j].chrom == s1_c[i].chrom and s2_c[j].start >= s1_c[i].end):
continue
# now everything at or after j in s2_c that starts before
# the end of s1_c must overlap with it
while s2_c[j].start < s1_c[i].end:
s = max(s1_c[i].start, s2_c[j].start)
e = min(s1_c[i].end, s2_c[j].end)
overlap = GenomicInterval(s1_c[i].chrom, s, e, "X", 0, "+")
if debug:
sys.stderr.write("\tadding to overlaps: " + str(overlap) + "\n")
res.append(overlap)
j += 1
if j >= len(s2_c) or s2_c[j].chrom != s1_c[i].chrom:
break
# it's possible the last intersecting element runs on to the
# next element from s1_c, so...
j -= 1
if debug:
sys.stderr.write("\tmoving s2_c index back to " + str(s2_c[j]) + "\n")
return res | python | def regionsIntersection(s1, s2, collapse=True):
"""
given two lists of genomic regions with chromosome, start and end
coordinates, return a new list of regions which is the intersection of those
two sets. Lists must be sorted by chromosome and start index
:return: new list that represents the intersection of the two input lists.
output regions will all have name "X", be on strand "+" and have
score 0
:param s1: first list of genomic regions
:param s2: second list of genomic regions
:raise GenomicIntervalError: if the input regions are not sorted correctly
(by chromosome and start index)
:note: O(n) time, O(n) space; informally, might use up to 3x space of input
"""
debug = False
# we don't need to explicitly check for sorting because sorted order is
# a post-condition of the collapsing function
s1_c = collapseRegions(s1)
s2_c = collapseRegions(s2)
if len(s1_c) == 0 or len(s2_c) == 0:
return []
res = []
j = 0
for i in range(0, len(s1_c)):
if debug:
sys.stderr.write("processing from s1_c : " + str(s1_c[i]) + "\n")
# find first thing in s2_c with end in or after s1_c[i]
if debug:
sys.stderr.write("i = " + str(i) + " and j = " + str(j) + "\n")
while (j < len(s2_c) and
(s2_c[j].chrom < s1_c[i].chrom or
(s2_c[j].chrom == s1_c[i].chrom and s2_c[j].end <= s1_c[i].start))):
j += 1
# nothing intersects if we hit the end of s2, or the end of the chrom,
# or we're still on the same chrom but start after the end of s2_c[i]
if j >= len(s2_c) or s2_c[j].chrom > s1_c[i].chrom or \
(s2_c[j].chrom == s1_c[i].chrom and s2_c[j].start >= s1_c[i].end):
continue
# now everything at or after j in s2_c that starts before
# the end of s1_c must overlap with it
while s2_c[j].start < s1_c[i].end:
s = max(s1_c[i].start, s2_c[j].start)
e = min(s1_c[i].end, s2_c[j].end)
overlap = GenomicInterval(s1_c[i].chrom, s, e, "X", 0, "+")
if debug:
sys.stderr.write("\tadding to overlaps: " + str(overlap) + "\n")
res.append(overlap)
j += 1
if j >= len(s2_c) or s2_c[j].chrom != s1_c[i].chrom:
break
# it's possible the last intersecting element runs on to the
# next element from s1_c, so...
j -= 1
if debug:
sys.stderr.write("\tmoving s2_c index back to " + str(s2_c[j]) + "\n")
return res | [
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] | given two lists of genomic regions with chromosome, start and end
coordinates, return a new list of regions which is the intersection of those
two sets. Lists must be sorted by chromosome and start index
:return: new list that represents the intersection of the two input lists.
output regions will all have name "X", be on strand "+" and have
score 0
:param s1: first list of genomic regions
:param s2: second list of genomic regions
:raise GenomicIntervalError: if the input regions are not sorted correctly
(by chromosome and start index)
:note: O(n) time, O(n) space; informally, might use up to 3x space of input | [
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] | fddae123b5d817daa39496183f19c000d9c3791f | https://github.com/pjuren/pyokit/blob/fddae123b5d817daa39496183f19c000d9c3791f/src/pyokit/datastruct/genomicInterval.py#L230-L293 |
247,067 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | bucketIterator | def bucketIterator(elements, buckets):
"""
For each bucket in buckets, yield it and any elements that overlap it.
:param elements: the genomic intervals to place into the buckets. Must be
sorted by chromosome and start index. This could be a
list, or an iterator.
:param buckets: the buckets into which genomic intervals should be binned.
Must be sorted by chromosome and start index. This could be
a list, or an iterator
:return: iterator that will yeild a tuple of 1 bucket and 1 list of elements
in the bucket for each call to __next__().
"""
def check_sorted(current, previous):
if (previous is not None) and \
((previous.chrom > current.chrom) or
((previous.chrom == current.chrom) and
(previous.start > current.start))):
raise GenomicIntervalError("elements not sorted. Saw " +
str(previous) + " before " + str(current))
def updateOpen(openHeap, elementIterator, bucketChrom,
bucketStart, bucketEnd):
"""
Drop elements from heap which start earlier than current bucket.
Update the open heap so that it contains only elements that end after the
start of the current bucket. Note that the heap may already contain some
elements that start after the end of the current bucket, if a previous
bucket ended after the end of this one and brought them into the set.
:param openHeap: a min heap of elements; uses the default sorting order
for the genomic intervals, which is by end index. This
is what we're updating.
:param elementIterator: an iterator from which we will pull new elements.
Elements yielded by this iterator must be sorted
by start index. Must be 'peakable'
:param bucketChrom: the chromosome of the current bucket.
:param bucketStart: the start index of the current bucket.
:param bucketEnd: the end index of the current bucket.
"""
# first, we're going to pop elements from the heap which can no longer
# overalp this or any future buckets. Buckets are sorted by start, so
# we'll never see another bucket that starts earlier than this one --
# hence any elements that end before the start of this bucket will never be
# used again and can be dropped. Elements in the heap are ordered by end
# index, so once we reach an element in the heap that does not end before
# the start of this bucket, we are sure that no others will come after it
# which do end before the start of this bucket. So we can stop dropping.
while len(openHeap) > 0 and ((openHeap[0].chrom < bucketChrom) or
((openHeap[0].chrom == bucketChrom) and
(openHeap[0].end <= bucketStart))):
heappop(openHeap)
# now we're going to add new elements from the iterator to the heap. As
# we know that elements in the iterator are sorted by start index, we know
# that once we see an element that has a start index greater than the end
# of this bucket, we can stop -- everything else after it will also start
# after the end of this bucket.
while (elementIterator.peek() is not None) and \
((elementIterator.peek().chrom < bucketChrom) or
((elementIterator.peek().chrom == bucketChrom) and
(elementIterator.peek().start < bucketEnd))):
e = elementIterator.__next__()
# if e falls before this bucket, we can skip it; buckets are sorted by
# start, so no other buckets start earlier than this one and so it
# cannot intersect any others.
if (e.chrom < bucketChrom) or \
(e.chrom == bucketChrom and e.end <= bucketStart):
continue
# now we know e intersects this bucket..
heappush(openHeap, e)
openElems = []
prevBucket = None
elementIter = AutoApplyIterator(elements, check_sorted)
for bucket in buckets:
# make sure the buckets are sorted by start index
if prevBucket is not None and ((bucket.chrom < prevBucket.chrom) or
(bucket.chrom == prevBucket.chrom and
bucket.start < prevBucket.start)):
raise GenomicIntervalError("regions-of-interest are not sorted. Saw " +
str(prevBucket) + " before " + str(bucket))
updateOpen(openElems, elementIter, bucket.chrom, bucket. start, bucket.end)
# be careful here not to leak a reference to the heap; if the caller
# decides to mess with that list, it'll screw us up. Anyway, we need a
# final check here to make sure we trim off any elements that exceed the
# end of this bucket.
yield bucket, [x for x in openElems if x.start < bucket.end]
prevBucket = bucket | python | def bucketIterator(elements, buckets):
"""
For each bucket in buckets, yield it and any elements that overlap it.
:param elements: the genomic intervals to place into the buckets. Must be
sorted by chromosome and start index. This could be a
list, or an iterator.
:param buckets: the buckets into which genomic intervals should be binned.
Must be sorted by chromosome and start index. This could be
a list, or an iterator
:return: iterator that will yeild a tuple of 1 bucket and 1 list of elements
in the bucket for each call to __next__().
"""
def check_sorted(current, previous):
if (previous is not None) and \
((previous.chrom > current.chrom) or
((previous.chrom == current.chrom) and
(previous.start > current.start))):
raise GenomicIntervalError("elements not sorted. Saw " +
str(previous) + " before " + str(current))
def updateOpen(openHeap, elementIterator, bucketChrom,
bucketStart, bucketEnd):
"""
Drop elements from heap which start earlier than current bucket.
Update the open heap so that it contains only elements that end after the
start of the current bucket. Note that the heap may already contain some
elements that start after the end of the current bucket, if a previous
bucket ended after the end of this one and brought them into the set.
:param openHeap: a min heap of elements; uses the default sorting order
for the genomic intervals, which is by end index. This
is what we're updating.
:param elementIterator: an iterator from which we will pull new elements.
Elements yielded by this iterator must be sorted
by start index. Must be 'peakable'
:param bucketChrom: the chromosome of the current bucket.
:param bucketStart: the start index of the current bucket.
:param bucketEnd: the end index of the current bucket.
"""
# first, we're going to pop elements from the heap which can no longer
# overalp this or any future buckets. Buckets are sorted by start, so
# we'll never see another bucket that starts earlier than this one --
# hence any elements that end before the start of this bucket will never be
# used again and can be dropped. Elements in the heap are ordered by end
# index, so once we reach an element in the heap that does not end before
# the start of this bucket, we are sure that no others will come after it
# which do end before the start of this bucket. So we can stop dropping.
while len(openHeap) > 0 and ((openHeap[0].chrom < bucketChrom) or
((openHeap[0].chrom == bucketChrom) and
(openHeap[0].end <= bucketStart))):
heappop(openHeap)
# now we're going to add new elements from the iterator to the heap. As
# we know that elements in the iterator are sorted by start index, we know
# that once we see an element that has a start index greater than the end
# of this bucket, we can stop -- everything else after it will also start
# after the end of this bucket.
while (elementIterator.peek() is not None) and \
((elementIterator.peek().chrom < bucketChrom) or
((elementIterator.peek().chrom == bucketChrom) and
(elementIterator.peek().start < bucketEnd))):
e = elementIterator.__next__()
# if e falls before this bucket, we can skip it; buckets are sorted by
# start, so no other buckets start earlier than this one and so it
# cannot intersect any others.
if (e.chrom < bucketChrom) or \
(e.chrom == bucketChrom and e.end <= bucketStart):
continue
# now we know e intersects this bucket..
heappush(openHeap, e)
openElems = []
prevBucket = None
elementIter = AutoApplyIterator(elements, check_sorted)
for bucket in buckets:
# make sure the buckets are sorted by start index
if prevBucket is not None and ((bucket.chrom < prevBucket.chrom) or
(bucket.chrom == prevBucket.chrom and
bucket.start < prevBucket.start)):
raise GenomicIntervalError("regions-of-interest are not sorted. Saw " +
str(prevBucket) + " before " + str(bucket))
updateOpen(openElems, elementIter, bucket.chrom, bucket. start, bucket.end)
# be careful here not to leak a reference to the heap; if the caller
# decides to mess with that list, it'll screw us up. Anyway, we need a
# final check here to make sure we trim off any elements that exceed the
# end of this bucket.
yield bucket, [x for x in openElems if x.start < bucket.end]
prevBucket = bucket | [
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:param elements: the genomic intervals to place into the buckets. Must be
sorted by chromosome and start index. This could be a
list, or an iterator.
:param buckets: the buckets into which genomic intervals should be binned.
Must be sorted by chromosome and start index. This could be
a list, or an iterator
:return: iterator that will yeild a tuple of 1 bucket and 1 list of elements
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247,068 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | parseWigString | def parseWigString(line, scoreType=int):
"""
Parse a string in simple Wig format and return a GenomicInterval.
:param line: the string to be parsed
:param scoreType: treat the score field as having this type.
:return: GenomicInterval object representing this wig line; the name of the
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"""
parts = line.split("\t")
if (len(parts) < 4):
raise GenomicIntervalError("failed to parse " + line +
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return GenomicInterval(parts[0].strip(), int(parts[1]), int(parts[2]), None,
scoreType(parts[3])) | python | def parseWigString(line, scoreType=int):
"""
Parse a string in simple Wig format and return a GenomicInterval.
:param line: the string to be parsed
:param scoreType: treat the score field as having this type.
:return: GenomicInterval object representing this wig line; the name of the
interval will be set to 'X', and it's strand to the default.
"""
parts = line.split("\t")
if (len(parts) < 4):
raise GenomicIntervalError("failed to parse " + line +
" as wig format, too few fields")
return GenomicInterval(parts[0].strip(), int(parts[1]), int(parts[2]), None,
scoreType(parts[3])) | [
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247,069 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | parseBEDString | def parseBEDString(line, scoreType=int, dropAfter=None):
"""
Parse a string in BED format and return a GenomicInterval object.
:param line: the string to be parsed
:param dropAfter: an int indicating that any fields after and including
this field should be ignored as they don't conform to
the BED format. By default, None, meaning we use all
fields. Index from zero.
:return: GenomicInterval object built from the BED string representation
"""
peices = line.split("\t")
if dropAfter is not None:
peices = peices[0:dropAfter]
if len(peices) < 3:
raise GenomicIntervalError("BED elements must have at least chrom, " +
"start and end; found only " +
str(len(peices)) + " in " + line)
chrom = peices[0]
start = peices[1]
end = peices[2]
name = None
score = None
strand = None
if len(peices) >= 4 is not None:
name = peices[3]
if len(peices) >= 5 is not None:
score = peices[4]
if len(peices) >= 6 is not None:
strand = peices[5]
return GenomicInterval(chrom, start, end, name, score, strand, scoreType) | python | def parseBEDString(line, scoreType=int, dropAfter=None):
"""
Parse a string in BED format and return a GenomicInterval object.
:param line: the string to be parsed
:param dropAfter: an int indicating that any fields after and including
this field should be ignored as they don't conform to
the BED format. By default, None, meaning we use all
fields. Index from zero.
:return: GenomicInterval object built from the BED string representation
"""
peices = line.split("\t")
if dropAfter is not None:
peices = peices[0:dropAfter]
if len(peices) < 3:
raise GenomicIntervalError("BED elements must have at least chrom, " +
"start and end; found only " +
str(len(peices)) + " in " + line)
chrom = peices[0]
start = peices[1]
end = peices[2]
name = None
score = None
strand = None
if len(peices) >= 4 is not None:
name = peices[3]
if len(peices) >= 5 is not None:
score = peices[4]
if len(peices) >= 6 is not None:
strand = peices[5]
return GenomicInterval(chrom, start, end, name, score, strand, scoreType) | [
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247,070 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | GenomicInterval.sameRegion | def sameRegion(self, e):
"""
Check whether self represents the same DNA region as e.
:param e: genomic region to compare against
:return: True if self and e are for the same region (ignores differences
in non-region related fields, such as name or score -- but does
consider strand)
"""
if e is None:
return False
return (self.chrom == e.chrom and self.start == e.start and
self.end == e.end and self.name == e.name and
self.strand == e.strand) | python | def sameRegion(self, e):
"""
Check whether self represents the same DNA region as e.
:param e: genomic region to compare against
:return: True if self and e are for the same region (ignores differences
in non-region related fields, such as name or score -- but does
consider strand)
"""
if e is None:
return False
return (self.chrom == e.chrom and self.start == e.start and
self.end == e.end and self.name == e.name and
self.strand == e.strand) | [
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247,071 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | GenomicInterval.__singleIntersect | def __singleIntersect(self, e):
"""
Get a list of GenomicRegions produced by subtracting e from self.
:return: a list of regions that represent the result of subtracting e from
self. The list might be empty if self is totally contained in e,
or may contain two elements if e is totally contained in self.
otherwise there'll be one element.
"""
if e.chrom != self.chrom or e.end < self.start or e.start > self.end:
# no intersection
return [copy.copy(self)]
if e.start <= self.start and e.end >= self.end:
# whole self is removed.
return []
if e.start > self.start and e.end < self.end:
# splits self in two
r1 = copy.copy(self)
r2 = copy.copy(self)
r1.end = e.start
r2.start = e.end
return [r1, r2]
if e.start <= self.start:
# cuts off start of self
r = copy.copy(self)
r.start = e.end
return [r]
if e.end >= self.end:
# cuts off end of self
r = copy.copy(self)
r.end = e.start
return [r]
# oops, we screwed up if we got to here..
raise GenomicIntervalError("fatal error - failed BED subtraction of " +
str(e) + " from " + str(self)) | python | def __singleIntersect(self, e):
"""
Get a list of GenomicRegions produced by subtracting e from self.
:return: a list of regions that represent the result of subtracting e from
self. The list might be empty if self is totally contained in e,
or may contain two elements if e is totally contained in self.
otherwise there'll be one element.
"""
if e.chrom != self.chrom or e.end < self.start or e.start > self.end:
# no intersection
return [copy.copy(self)]
if e.start <= self.start and e.end >= self.end:
# whole self is removed.
return []
if e.start > self.start and e.end < self.end:
# splits self in two
r1 = copy.copy(self)
r2 = copy.copy(self)
r1.end = e.start
r2.start = e.end
return [r1, r2]
if e.start <= self.start:
# cuts off start of self
r = copy.copy(self)
r.start = e.end
return [r]
if e.end >= self.end:
# cuts off end of self
r = copy.copy(self)
r.end = e.start
return [r]
# oops, we screwed up if we got to here..
raise GenomicIntervalError("fatal error - failed BED subtraction of " +
str(e) + " from " + str(self)) | [
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247,072 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | GenomicInterval.subtract | def subtract(self, es):
"""
Subtract the BED elements in es from self.
:param es: a list of BED elements (or anything with chrom, start, end)
:return: a list of BED elements which represent what is left of
self after the subtraction. This might be an empty list.
"""
workingSet = [self]
for e in es:
newWorkingSet = []
for w in workingSet:
newWorkingSet += w.__singleIntersect(e)
workingSet = newWorkingSet
return workingSet | python | def subtract(self, es):
"""
Subtract the BED elements in es from self.
:param es: a list of BED elements (or anything with chrom, start, end)
:return: a list of BED elements which represent what is left of
self after the subtraction. This might be an empty list.
"""
workingSet = [self]
for e in es:
newWorkingSet = []
for w in workingSet:
newWorkingSet += w.__singleIntersect(e)
workingSet = newWorkingSet
return workingSet | [
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247,073 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | GenomicInterval.sizeOfOverlap | def sizeOfOverlap(self, e):
"""
Get the size of the overlap between self and e.
:return: the number of bases that are shared in common between self and e.
"""
# no overlap
if not self.intersects(e):
return 0
# complete inclusion..
if e.start >= self.start and e.end <= self.end:
return len(e)
if self.start >= e.start and self.end <= e.end:
return len(self)
# partial overlap
if e.start > self.start:
return (self.end - e.start)
if self.start > e.start:
return (e.end - self.start) | python | def sizeOfOverlap(self, e):
"""
Get the size of the overlap between self and e.
:return: the number of bases that are shared in common between self and e.
"""
# no overlap
if not self.intersects(e):
return 0
# complete inclusion..
if e.start >= self.start and e.end <= self.end:
return len(e)
if self.start >= e.start and self.end <= e.end:
return len(self)
# partial overlap
if e.start > self.start:
return (self.end - e.start)
if self.start > e.start:
return (e.end - self.start) | [
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247,074 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | GenomicInterval.intersects | def intersects(self, e):
"""
Check whether e intersects self.
:return: true if this elements intersects the element e
"""
if self.chrom != e.chrom:
return False
if e.start >= self.start and e.start < self.end:
return True
if e.end > self.start and e.end <= self.end:
return True
if e.start < self.start and e.end > self.end:
return True
return False | python | def intersects(self, e):
"""
Check whether e intersects self.
:return: true if this elements intersects the element e
"""
if self.chrom != e.chrom:
return False
if e.start >= self.start and e.start < self.end:
return True
if e.end > self.start and e.end <= self.end:
return True
if e.start < self.start and e.end > self.end:
return True
return False | [
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247,075 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | GenomicInterval.isPositiveStrand | def isPositiveStrand(self):
"""
Check if this genomic region is on the positive strand.
:return: True if this element is on the positive strand
"""
if self.strand is None and self.DEFAULT_STRAND == self.POSITIVE_STRAND:
return True
return self.strand == self.POSITIVE_STRAND | python | def isPositiveStrand(self):
"""
Check if this genomic region is on the positive strand.
:return: True if this element is on the positive strand
"""
if self.strand is None and self.DEFAULT_STRAND == self.POSITIVE_STRAND:
return True
return self.strand == self.POSITIVE_STRAND | [
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247,076 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | GenomicInterval.isNegativeStrand | def isNegativeStrand(self):
"""
Check if this genomic interval is on the negative strand.
:return: True if this element is on the negative strand
"""
if self.strand is None and self.DEFAULT_STRAND == self.NEGATIVE_STRAND:
return True
return self.strand == self.NEGATIVE_STRAND | python | def isNegativeStrand(self):
"""
Check if this genomic interval is on the negative strand.
:return: True if this element is on the negative strand
"""
if self.strand is None and self.DEFAULT_STRAND == self.NEGATIVE_STRAND:
return True
return self.strand == self.NEGATIVE_STRAND | [
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247,077 | pjuren/pyokit | src/pyokit/datastruct/genomicInterval.py | GenomicInterval.transform_center | def transform_center(self, size):
"""
Tranform self so it is centered on the same spot, but has new size.
If the region grows, the extra nucleotides will be distributed evenly to
the 5' and 3' side of the current region if possible. If the extra is odd,
the 3' side will get the extra one. Similarly, if the resize shrinks the
interval, bases will be removed from the 5' and 3' sides equally; if the
number to remove is odd, the extra one will be removed from the 3' side.
:param size: size of the region after transformation.
"""
if size < 1:
raise GenomicIntervalError("Cannot resize genomic interval to " +
str(size) + " bases; must be at least 1 " +
"base in length")
if size == len(self):
return
elif size > len(self):
extra = size - len(self)
extra_5_prime = extra / 2
extra_3_prime = extra / 2 if extra % 2 == 0 else (extra / 2) + 1
assert(extra_5_prime + extra_3_prime == extra)
self.start = (self.start - extra_5_prime if self.isPositiveStrand()
else self.start - extra_3_prime)
self.end = (self.end + extra_3_prime if self.isPositiveStrand()
else self.end + extra_5_prime)
else:
less = len(self) - size
less_5_prime = less / 2
less_3_prime = less / 2 if less % 2 == 0 else (less / 2) + 1
assert(less_5_prime + less_3_prime == less)
self.start = (self.start + less_5_prime if self.isPositiveStrand()
else self.start + less_3_prime)
self.end = (self.end - less_3_prime if self.isPositiveStrand()
else self.end - less_5_prime) | python | def transform_center(self, size):
"""
Tranform self so it is centered on the same spot, but has new size.
If the region grows, the extra nucleotides will be distributed evenly to
the 5' and 3' side of the current region if possible. If the extra is odd,
the 3' side will get the extra one. Similarly, if the resize shrinks the
interval, bases will be removed from the 5' and 3' sides equally; if the
number to remove is odd, the extra one will be removed from the 3' side.
:param size: size of the region after transformation.
"""
if size < 1:
raise GenomicIntervalError("Cannot resize genomic interval to " +
str(size) + " bases; must be at least 1 " +
"base in length")
if size == len(self):
return
elif size > len(self):
extra = size - len(self)
extra_5_prime = extra / 2
extra_3_prime = extra / 2 if extra % 2 == 0 else (extra / 2) + 1
assert(extra_5_prime + extra_3_prime == extra)
self.start = (self.start - extra_5_prime if self.isPositiveStrand()
else self.start - extra_3_prime)
self.end = (self.end + extra_3_prime if self.isPositiveStrand()
else self.end + extra_5_prime)
else:
less = len(self) - size
less_5_prime = less / 2
less_3_prime = less / 2 if less % 2 == 0 else (less / 2) + 1
assert(less_5_prime + less_3_prime == less)
self.start = (self.start + less_5_prime if self.isPositiveStrand()
else self.start + less_3_prime)
self.end = (self.end - less_3_prime if self.isPositiveStrand()
else self.end - less_5_prime) | [
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247,078 | minhhoit/yacms | yacms/accounts/admin.py | UserProfileAdmin.save_model | def save_model(self, request, obj, form, change):
"""
If the ``ACCOUNTS_APPROVAL_REQUIRED`` setting is ``True``,
send a notification email to the user being saved if their
``active`` status has changed to ``True``.
If the ``ACCOUNTS_VERIFICATION_REQUIRED`` setting is ``True``,
send a verification email instead.
"""
must_send_verification_mail_after_save = False
if change and settings.ACCOUNTS_APPROVAL_REQUIRED:
if obj.is_active and not User.objects.get(id=obj.id).is_active:
if settings.ACCOUNTS_VERIFICATION_REQUIRED:
# Accounts verification requires an inactive account
obj.is_active = False
# The token generated by send_verification_mail()
# must match the _saved_ User object,
# so postpone send_verification_mail() until later
must_send_verification_mail_after_save = True
else:
send_approved_mail(request, obj)
super(UserProfileAdmin, self).save_model(request, obj, form, change)
if must_send_verification_mail_after_save:
user = User.objects.get(id=obj.id)
send_verification_mail(request, user, "signup_verify") | python | def save_model(self, request, obj, form, change):
"""
If the ``ACCOUNTS_APPROVAL_REQUIRED`` setting is ``True``,
send a notification email to the user being saved if their
``active`` status has changed to ``True``.
If the ``ACCOUNTS_VERIFICATION_REQUIRED`` setting is ``True``,
send a verification email instead.
"""
must_send_verification_mail_after_save = False
if change and settings.ACCOUNTS_APPROVAL_REQUIRED:
if obj.is_active and not User.objects.get(id=obj.id).is_active:
if settings.ACCOUNTS_VERIFICATION_REQUIRED:
# Accounts verification requires an inactive account
obj.is_active = False
# The token generated by send_verification_mail()
# must match the _saved_ User object,
# so postpone send_verification_mail() until later
must_send_verification_mail_after_save = True
else:
send_approved_mail(request, obj)
super(UserProfileAdmin, self).save_model(request, obj, form, change)
if must_send_verification_mail_after_save:
user = User.objects.get(id=obj.id)
send_verification_mail(request, user, "signup_verify") | [
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If the ``ACCOUNTS_VERIFICATION_REQUIRED`` setting is ``True``,
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247,079 | malthe/pop | src/pop/services/common.py | Service.deploy | def deploy(self, machine):
"""Deploy service."""
log.debug("machine id: %s." % machine)
path = self.path + "/machines"
value, metadata = yield self.client.get(path)
machines = json.loads(value)
machines.append(machine)
yield self.client.set(path, json.dumps(machines)) | python | def deploy(self, machine):
"""Deploy service."""
log.debug("machine id: %s." % machine)
path = self.path + "/machines"
value, metadata = yield self.client.get(path)
machines = json.loads(value)
machines.append(machine)
yield self.client.set(path, json.dumps(machines)) | [
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247,080 | malthe/pop | src/pop/services/common.py | Service.add | def add(self):
"""Add service definition to hierarchy."""
yield self.client.create(self.path)
yield self.client.create(self.path + "/type", self.name)
yield self.client.create(self.path + "/state")
yield self.client.create(self.path + "/machines", "[]")
log.debug("registered service '%s' at %s." % (self.name, self.path)) | python | def add(self):
"""Add service definition to hierarchy."""
yield self.client.create(self.path)
yield self.client.create(self.path + "/type", self.name)
yield self.client.create(self.path + "/state")
yield self.client.create(self.path + "/machines", "[]")
log.debug("registered service '%s' at %s." % (self.name, self.path)) | [
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247,081 | OpenGov/python_data_wrap | datawrap/basewrap.py | UnorderedCachedDict._insert_cache | def _insert_cache(self, key, val, read):
'''
Does an insert into the cache such that the cache
will have an updated entry for the key,value,read
tuple. Any changes to those values will both update
the local cache and queue any required writes to the
database.
'''
if key != None and self.stringify_keys:
key = str(key)
cval = self._cache.get(key)
if cval == None:
self._cur_size += 1
if cval == None or val != cval:
self._cache[key] = val
# Force a write if it's a write or if it's
# unclear that the item was modified
if not self.read_only and (not self._immutable_vals or not read):
self._wqueue.add(key) | python | def _insert_cache(self, key, val, read):
'''
Does an insert into the cache such that the cache
will have an updated entry for the key,value,read
tuple. Any changes to those values will both update
the local cache and queue any required writes to the
database.
'''
if key != None and self.stringify_keys:
key = str(key)
cval = self._cache.get(key)
if cval == None:
self._cur_size += 1
if cval == None or val != cval:
self._cache[key] = val
# Force a write if it's a write or if it's
# unclear that the item was modified
if not self.read_only and (not self._immutable_vals or not read):
self._wqueue.add(key) | [
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247,082 | OpenGov/python_data_wrap | datawrap/basewrap.py | UnorderedCachedDict._sync_writes | def _sync_writes(self):
'''
Flushes the write queue
'''
for key in self._wqueue:
val = self._cache[key]
self._database[key] = val
del self._wqueue
self._wqueue = set()
self._database.sync() | python | def _sync_writes(self):
'''
Flushes the write queue
'''
for key in self._wqueue:
val = self._cache[key]
self._database[key] = val
del self._wqueue
self._wqueue = set()
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247,083 | OpenGov/python_data_wrap | datawrap/basewrap.py | UnorderedCachedDict.drop_cache | def drop_cache(self):
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'''
Drops all changes in the cache.
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del self._cache
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247,084 | OpenGov/python_data_wrap | datawrap/basewrap.py | UnorderedCachedSet.update | def update(self, *args, **kwargs):
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'''
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'''
Updates the set to include all arguments passed in. If the keyword
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'''
preprocess = kwargs.get('preprocess')
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247,085 | darkfeline/mir.anidb | mir/anidb/anime.py | get_episode_number | def get_episode_number(episode: Episode) -> int:
"""Get the episode number.
The episode number is unique for an anime and episode type, but not
across episode types for the same anime.
"""
match = _NUMBER_SUFFIX.search(episode.epno)
return int(match.group(1)) | python | def get_episode_number(episode: Episode) -> int:
"""Get the episode number.
The episode number is unique for an anime and episode type, but not
across episode types for the same anime.
"""
match = _NUMBER_SUFFIX.search(episode.epno)
return int(match.group(1)) | [
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247,086 | darkfeline/mir.anidb | mir/anidb/anime.py | get_episode_title | def get_episode_title(episode: Episode) -> int:
"""Get the episode title.
Japanese title is prioritized.
"""
for title in episode.titles:
if title.lang == 'ja':
return title.title
else:
return episode.titles[0].title | python | def get_episode_title(episode: Episode) -> int:
"""Get the episode title.
Japanese title is prioritized.
"""
for title in episode.titles:
if title.lang == 'ja':
return title.title
else:
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247,087 | darkfeline/mir.anidb | mir/anidb/anime.py | _find_element_text | def _find_element_text(element, match, default=None):
"""Find a matching subelement and return its text.
If default is given, return it if a matching subelement is not
found. Otherwise, ValueError is raised.
"""
child = element.find(match)
try:
return child.text
except AttributeError:
if default is not None:
return default
else:
raise MissingElementError(element, match) | python | def _find_element_text(element, match, default=None):
"""Find a matching subelement and return its text.
If default is given, return it if a matching subelement is not
found. Otherwise, ValueError is raised.
"""
child = element.find(match)
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247,088 | darkfeline/mir.anidb | mir/anidb/anime.py | _unpack_episode | def _unpack_episode(element: ET.Element):
"""Unpack Episode from episode XML element."""
return Episode(
epno=element.find('epno').text,
type=int(element.find('epno').get('type')),
length=int(element.find('length').text),
titles=tuple(_unpack_episode_title(title)
for title in element.iterfind('title')),
) | python | def _unpack_episode(element: ET.Element):
"""Unpack Episode from episode XML element."""
return Episode(
epno=element.find('epno').text,
type=int(element.find('epno').get('type')),
length=int(element.find('length').text),
titles=tuple(_unpack_episode_title(title)
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247,089 | darkfeline/mir.anidb | mir/anidb/anime.py | _unpack_episode_title | def _unpack_episode_title(element: ET.Element):
"""Unpack EpisodeTitle from title XML element."""
return EpisodeTitle(title=element.text,
lang=element.get(f'{XML}lang')) | python | def _unpack_episode_title(element: ET.Element):
"""Unpack EpisodeTitle from title XML element."""
return EpisodeTitle(title=element.text,
lang=element.get(f'{XML}lang')) | [
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247,090 | openpermissions/perch | perch/model.py | Document.validate | def validate(self):
"""Validate the resource using its voluptuous schema"""
try:
# update _resource to have default values from the schema
self._resource = self.schema(self._resource)
except MultipleInvalid as e:
errors = [format_error(err, self.resource_type) for err in e.errors]
raise exceptions.ValidationError({'errors': errors})
yield self.check_unique() | python | def validate(self):
"""Validate the resource using its voluptuous schema"""
try:
# update _resource to have default values from the schema
self._resource = self.schema(self._resource)
except MultipleInvalid as e:
errors = [format_error(err, self.resource_type) for err in e.errors]
raise exceptions.ValidationError({'errors': errors})
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247,091 | openpermissions/perch | perch/model.py | Document._save | def _save(self):
"""
Save the resource
It's better to use the create, updated & delete methods intsead of
modifying an instance and calling save, because then we call the
can_create, can_update & can_delete methods to check whether a user
is permitted to make the changes.
"""
yield self.validate()
db = self.db_client()
saved = yield db.save_doc(self._resource)
# Allow couch to create Document IDs
if '_id' not in self._resource:
self._resource['_id'] = saved['id'] | python | def _save(self):
"""
Save the resource
It's better to use the create, updated & delete methods intsead of
modifying an instance and calling save, because then we call the
can_create, can_update & can_delete methods to check whether a user
is permitted to make the changes.
"""
yield self.validate()
db = self.db_client()
saved = yield db.save_doc(self._resource)
# Allow couch to create Document IDs
if '_id' not in self._resource:
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247,092 | openpermissions/perch | perch/model.py | Document.save_subresource | def save_subresource(self, subresource):
"""
Save the sub-resource
NOTE: Currently assumes subresources are stored within a dictionary,
keyed with the subresource's ID
"""
data = deepcopy(subresource._resource)
data.pop('id', None)
data.pop(self.resource_type + '_id', None)
subresources = getattr(self, subresource.parent_key, {})
subresources[subresource.id] = data
setattr(self, subresource.parent_key, subresources)
yield self._save() | python | def save_subresource(self, subresource):
"""
Save the sub-resource
NOTE: Currently assumes subresources are stored within a dictionary,
keyed with the subresource's ID
"""
data = deepcopy(subresource._resource)
data.pop('id', None)
data.pop(self.resource_type + '_id', None)
subresources = getattr(self, subresource.parent_key, {})
subresources[subresource.id] = data
setattr(self, subresource.parent_key, subresources)
yield self._save() | [
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247,093 | openpermissions/perch | perch/model.py | Document.delete | def delete(self, user):
"""Delete a resource"""
if user:
can_delete = yield self.can_delete(user)
else:
can_delete = False
if not can_delete:
raise exceptions.Unauthorized('User may not delete the resource')
doc = {
'_id': self.id,
'_deleted': True
}
try:
doc['_rev'] = self._rev
except AttributeError:
pass
db = self.db_client()
yield db.save_doc(doc)
self._resource = doc | python | def delete(self, user):
"""Delete a resource"""
if user:
can_delete = yield self.can_delete(user)
else:
can_delete = False
if not can_delete:
raise exceptions.Unauthorized('User may not delete the resource')
doc = {
'_id': self.id,
'_deleted': True
}
try:
doc['_rev'] = self._rev
except AttributeError:
pass
db = self.db_client()
yield db.save_doc(doc)
self._resource = doc | [
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247,094 | openpermissions/perch | perch/model.py | Document.delete_subresource | def delete_subresource(self, subresource):
"""
Delete the sub-resource
NOTE: Currently assumes subresources are stored within a dictionary,
keyed with the subresource's ID
"""
subresources = getattr(self, subresource.parent_key, {})
del subresources[subresource.id]
yield self._save() | python | def delete_subresource(self, subresource):
"""
Delete the sub-resource
NOTE: Currently assumes subresources are stored within a dictionary,
keyed with the subresource's ID
"""
subresources = getattr(self, subresource.parent_key, {})
del subresources[subresource.id]
yield self._save() | [
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247,095 | openpermissions/perch | perch/model.py | Document.state | def state(self):
"""Get the Document's state"""
state = self._resource.get('state', self.default_state)
if state in State:
return state
else:
return getattr(State, state) | python | def state(self):
"""Get the Document's state"""
state = self._resource.get('state', self.default_state)
if state in State:
return state
else:
return getattr(State, state) | [
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247,096 | openpermissions/perch | perch/model.py | SubResource.get_parent | def get_parent(self):
"""
Get the parent resource from the database
The get, create & update methods will populate the parent for you. Use
this method in the cases where parent has not been populated.
"""
if not self._parent:
self._parent = yield self.parent_resource.get(self.parent_id)
raise Return(self._parent) | python | def get_parent(self):
"""
Get the parent resource from the database
The get, create & update methods will populate the parent for you. Use
this method in the cases where parent has not been populated.
"""
if not self._parent:
self._parent = yield self.parent_resource.get(self.parent_id)
raise Return(self._parent) | [
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247,097 | openpermissions/perch | perch/model.py | SubResource.parent_resources | def parent_resources(cls):
"""Get a list of parent resources, starting from the Document"""
parent = cls.parent_resource
parents = [parent]
try:
while True:
parent = parent.parent_resource
parents.append(parent)
except AttributeError:
pass
parents.reverse()
return parents | python | def parent_resources(cls):
"""Get a list of parent resources, starting from the Document"""
parent = cls.parent_resource
parents = [parent]
try:
while True:
parent = parent.parent_resource
parents.append(parent)
except AttributeError:
pass
parents.reverse()
return parents | [
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247,098 | openpermissions/perch | perch/model.py | SubResource.create | def create(cls, user, **kwargs):
"""If parent resource is not an editable state, should not be able to create."""
parent_id = kwargs.get(cls.parent_resource.resource_type + '_id')
try:
parent = yield cls.parent_resource.get(parent_id)
except couch.NotFound:
msg = 'Parent {} with id {} not found'.format(
cls.parent_resource.resource_type,
parent_id)
raise exceptions.ValidationError(msg)
if not parent.editable:
err = 'Cannot create child of {} resource'.format(parent.state.name)
raise exceptions.Unauthorized(err)
resource = yield super(SubResource, cls).create(user, **kwargs)
resource._parent = parent
raise Return(resource) | python | def create(cls, user, **kwargs):
"""If parent resource is not an editable state, should not be able to create."""
parent_id = kwargs.get(cls.parent_resource.resource_type + '_id')
try:
parent = yield cls.parent_resource.get(parent_id)
except couch.NotFound:
msg = 'Parent {} with id {} not found'.format(
cls.parent_resource.resource_type,
parent_id)
raise exceptions.ValidationError(msg)
if not parent.editable:
err = 'Cannot create child of {} resource'.format(parent.state.name)
raise exceptions.Unauthorized(err)
resource = yield super(SubResource, cls).create(user, **kwargs)
resource._parent = parent
raise Return(resource) | [
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247,099 | openpermissions/perch | perch/model.py | SubResource.update | def update(self, user, **kwargs):
"""If parent resource is not an editable state, should not be able to update"""
yield self.get_parent()
if not self.parent.editable:
err = 'Cannot update child of {} resource'.format(self.parent.state.name)
raise exceptions.Unauthorized(err)
yield super(SubResource, self).update(user, **kwargs) | python | def update(self, user, **kwargs):
"""If parent resource is not an editable state, should not be able to update"""
yield self.get_parent()
if not self.parent.editable:
err = 'Cannot update child of {} resource'.format(self.parent.state.name)
raise exceptions.Unauthorized(err)
yield super(SubResource, self).update(user, **kwargs) | [
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