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mattlong/hermes | hermes/chatroom.py | Chatroom.on_presence | def on_presence(self, session, presence):
"""Handles presence stanzas"""
from_jid = presence.getFrom()
is_member = self.is_member(from_jid.getStripped())
if is_member:
member = self.get_member(from_jid.getStripped())
else:
member = None
logger.info('presence: from=%s is_member=%s type=%s' % (from_jid, is_member, presence.getType()))
if presence.getType() == 'subscribed':
if is_member:
logger.info('[%s] accepted their invitation' % (from_jid,))
member['STATUS'] = 'ACTIVE'
else:
#TODO: user accepted, but is no longer be on the roster, unsubscribe?
pass
elif presence.getType() == 'subscribe':
if is_member:
logger.info('Acknowledging subscription request from [%s]' % (from_jid,))
self.client.sendPresence(jid=from_jid, typ='subscribed')
member['STATUS'] = 'ACTIVE'
self.broadcast('%s has accepted their invitation!' % (from_jid,))
else:
#TODO: show that a user has requested membership?
pass
elif presence.getType() == None:
if is_member:
member['ONLINE'] += 1
elif presence.getType() == 'unavailable':
if is_member:
member['ONLINE'] -= 1
else:
logger.info('Unhandled presence stanza of type [%s] from [%s]' % (presence.getType(), from_jid)) | python | def on_presence(self, session, presence):
"""Handles presence stanzas"""
from_jid = presence.getFrom()
is_member = self.is_member(from_jid.getStripped())
if is_member:
member = self.get_member(from_jid.getStripped())
else:
member = None
logger.info('presence: from=%s is_member=%s type=%s' % (from_jid, is_member, presence.getType()))
if presence.getType() == 'subscribed':
if is_member:
logger.info('[%s] accepted their invitation' % (from_jid,))
member['STATUS'] = 'ACTIVE'
else:
#TODO: user accepted, but is no longer be on the roster, unsubscribe?
pass
elif presence.getType() == 'subscribe':
if is_member:
logger.info('Acknowledging subscription request from [%s]' % (from_jid,))
self.client.sendPresence(jid=from_jid, typ='subscribed')
member['STATUS'] = 'ACTIVE'
self.broadcast('%s has accepted their invitation!' % (from_jid,))
else:
#TODO: show that a user has requested membership?
pass
elif presence.getType() == None:
if is_member:
member['ONLINE'] += 1
elif presence.getType() == 'unavailable':
if is_member:
member['ONLINE'] -= 1
else:
logger.info('Unhandled presence stanza of type [%s] from [%s]' % (presence.getType(), from_jid)) | [
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"Handles",
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"stanzas"
] | 63a5afcafe90ca99aeb44edeee9ed6f90baae431 | https://github.com/mattlong/hermes/blob/63a5afcafe90ca99aeb44edeee9ed6f90baae431/hermes/chatroom.py#L179-L213 | train |
mattlong/hermes | hermes/chatroom.py | Chatroom.on_message | def on_message(self, con, event):
"""Handles messge stanzas"""
msg_type = event.getType()
nick = event.getFrom().getResource()
from_jid = event.getFrom().getStripped()
body = event.getBody()
if msg_type == 'chat' and body is None:
return
logger.debug('msg_type[%s] from[%s] nick[%s] body[%s]' % (msg_type, from_jid, nick, body,))
sender = filter(lambda m: m['JID'] == from_jid, self.params['MEMBERS'])
should_process = msg_type in ['message', 'chat', None] and body is not None and len(sender) == 1
if not should_process: return
sender = sender[0]
try:
for p in self.command_patterns:
reg, cmd = p
m = reg.match(body)
if m:
logger.info('pattern matched for bot command \'%s\'' % (cmd,))
function = getattr(self, str(cmd), None)
if function:
return function(sender, body, m)
words = body.split(' ')
cmd, args = words[0], words[1:]
if cmd and cmd[0] == '/':
cmd = cmd[1:]
command_handler = getattr(self, 'do_'+cmd, None)
if command_handler:
return command_handler(sender, body, args)
broadcast_body = '[%s] %s' % (sender['NICK'], body,)
return self.broadcast(broadcast_body, exclude=(sender,))
except:
logger.exception('Error handling message [%s] from [%s]' % (body, sender['JID'])) | python | def on_message(self, con, event):
"""Handles messge stanzas"""
msg_type = event.getType()
nick = event.getFrom().getResource()
from_jid = event.getFrom().getStripped()
body = event.getBody()
if msg_type == 'chat' and body is None:
return
logger.debug('msg_type[%s] from[%s] nick[%s] body[%s]' % (msg_type, from_jid, nick, body,))
sender = filter(lambda m: m['JID'] == from_jid, self.params['MEMBERS'])
should_process = msg_type in ['message', 'chat', None] and body is not None and len(sender) == 1
if not should_process: return
sender = sender[0]
try:
for p in self.command_patterns:
reg, cmd = p
m = reg.match(body)
if m:
logger.info('pattern matched for bot command \'%s\'' % (cmd,))
function = getattr(self, str(cmd), None)
if function:
return function(sender, body, m)
words = body.split(' ')
cmd, args = words[0], words[1:]
if cmd and cmd[0] == '/':
cmd = cmd[1:]
command_handler = getattr(self, 'do_'+cmd, None)
if command_handler:
return command_handler(sender, body, args)
broadcast_body = '[%s] %s' % (sender['NICK'], body,)
return self.broadcast(broadcast_body, exclude=(sender,))
except:
logger.exception('Error handling message [%s] from [%s]' % (body, sender['JID'])) | [
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] | 63a5afcafe90ca99aeb44edeee9ed6f90baae431 | https://github.com/mattlong/hermes/blob/63a5afcafe90ca99aeb44edeee9ed6f90baae431/hermes/chatroom.py#L215-L254 | train |
cloudmesh-cmd3/cmd3 | cmd3/plugins/activate.py | activate.activate | def activate(self):
"""method to activate all activation methods in the shell and
its plugins.
"""
d = dir(self)
self.plugins = []
for key in d:
if key.startswith("shell_activate_"):
if self.echo:
Console.ok("Shell Activate: {0}".format(key))
self.plugins.append(key)
for key in d:
if key.startswith("activate_"):
if self.echo:
Console.ok("Activate: {0}".format(key))
self.plugins.append(key)
for key in self.plugins:
if self.echo:
Console.ok("> {0}".format(key.replace("_", " ", 1)))
exec ("self.%s()" % key) | python | def activate(self):
"""method to activate all activation methods in the shell and
its plugins.
"""
d = dir(self)
self.plugins = []
for key in d:
if key.startswith("shell_activate_"):
if self.echo:
Console.ok("Shell Activate: {0}".format(key))
self.plugins.append(key)
for key in d:
if key.startswith("activate_"):
if self.echo:
Console.ok("Activate: {0}".format(key))
self.plugins.append(key)
for key in self.plugins:
if self.echo:
Console.ok("> {0}".format(key.replace("_", " ", 1)))
exec ("self.%s()" % key) | [
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cloudmesh-cmd3/cmd3 | cmd3/plugins/activate.py | activate.do_help | def do_help(self, arg):
"""List available commands with "help" or detailed help with "help cmd"."""
if arg:
# XXX check arg syntax
try:
func = getattr(self, 'help_' + arg)
except AttributeError:
try:
doc = getattr(self, 'do_' + arg).__doc__
if doc:
self.stdout.write("%s\n" % str(doc))
return
except AttributeError:
pass
self.stdout.write("%s\n" % str(self.nohelp % (arg,)))
return
func()
else:
names = self.get_names()
cmds_doc = []
cmds_undoc = []
help_page = {}
for name in names:
if name[:5] == 'help_':
help_page[name[5:]] = 1
names.sort()
# There can be duplicates if routines overridden
prevname = ''
for name in names:
if name[:3] == 'do_':
if name == prevname:
continue
prevname = name
cmd = name[3:]
if cmd in help_page:
cmds_doc.append(cmd)
del help_page[cmd]
elif getattr(self, name).__doc__:
cmds_doc.append(cmd)
else:
cmds_undoc.append(cmd)
self.stdout.write("%s\n" % str(self.doc_leader))
self.print_topics(self.doc_header, cmds_doc, 15, 80)
self.print_topics(self.misc_header, list(help_page.keys()), 15, 80)
self.print_topics(self.undoc_header, cmds_undoc, 15, 80)
for topic in self.command_topics:
topic_cmds = self.command_topics[topic]
self.print_topics(string.capwords(topic + " commands"), topic_cmds, 15, 80) | python | def do_help(self, arg):
"""List available commands with "help" or detailed help with "help cmd"."""
if arg:
# XXX check arg syntax
try:
func = getattr(self, 'help_' + arg)
except AttributeError:
try:
doc = getattr(self, 'do_' + arg).__doc__
if doc:
self.stdout.write("%s\n" % str(doc))
return
except AttributeError:
pass
self.stdout.write("%s\n" % str(self.nohelp % (arg,)))
return
func()
else:
names = self.get_names()
cmds_doc = []
cmds_undoc = []
help_page = {}
for name in names:
if name[:5] == 'help_':
help_page[name[5:]] = 1
names.sort()
# There can be duplicates if routines overridden
prevname = ''
for name in names:
if name[:3] == 'do_':
if name == prevname:
continue
prevname = name
cmd = name[3:]
if cmd in help_page:
cmds_doc.append(cmd)
del help_page[cmd]
elif getattr(self, name).__doc__:
cmds_doc.append(cmd)
else:
cmds_undoc.append(cmd)
self.stdout.write("%s\n" % str(self.doc_leader))
self.print_topics(self.doc_header, cmds_doc, 15, 80)
self.print_topics(self.misc_header, list(help_page.keys()), 15, 80)
self.print_topics(self.undoc_header, cmds_undoc, 15, 80)
for topic in self.command_topics:
topic_cmds = self.command_topics[topic]
self.print_topics(string.capwords(topic + " commands"), topic_cmds, 15, 80) | [
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b10m/ziggo_mediabox_xl | ziggo_mediabox_xl.py | ZiggoMediaboxXL._fetch_channels | def _fetch_channels(self):
"""Retrieve Ziggo channel information."""
json = requests.get(self._channels_url).json()
self._channels = {c['channel']['code']: c['channel']['name']
for c in json['channels']} | python | def _fetch_channels(self):
"""Retrieve Ziggo channel information."""
json = requests.get(self._channels_url).json()
self._channels = {c['channel']['code']: c['channel']['name']
for c in json['channels']} | [
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b10m/ziggo_mediabox_xl | ziggo_mediabox_xl.py | ZiggoMediaboxXL.send_keys | def send_keys(self, keys):
"""Send keys to the device."""
try:
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
sock.settimeout(self._timeout)
sock.connect((self._ip, self._port['cmd']))
# mandatory dance
version_info = sock.recv(15)
sock.send(version_info)
sock.recv(2)
sock.send(bytes.fromhex('01'))
sock.recv(4)
sock.recv(24)
# send our command now!
for key in keys:
if key in self._keys:
sock.send(bytes.fromhex("04 01 00 00 00 00 " +
self._keys[key]))
sock.send(bytes.fromhex("04 00 00 00 00 00 " +
self._keys[key]))
sock.close()
except socket.error:
raise | python | def send_keys(self, keys):
"""Send keys to the device."""
try:
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
sock.settimeout(self._timeout)
sock.connect((self._ip, self._port['cmd']))
# mandatory dance
version_info = sock.recv(15)
sock.send(version_info)
sock.recv(2)
sock.send(bytes.fromhex('01'))
sock.recv(4)
sock.recv(24)
# send our command now!
for key in keys:
if key in self._keys:
sock.send(bytes.fromhex("04 01 00 00 00 00 " +
self._keys[key]))
sock.send(bytes.fromhex("04 00 00 00 00 00 " +
self._keys[key]))
sock.close()
except socket.error:
raise | [
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mbourqui/django-echoices | echoices/fields/fields.py | make_echoicefield | def make_echoicefield(echoices, *args, klass_name=None, **kwargs):
"""
Construct a subclass of a derived `models.Field` specific to the type of the `EChoice` values.
Parameters
----------
echoices : subclass of EChoice
args
Passed to the derived `models.Field`
klass_name : str
Give a specific name to the returned class.
By default for Django < 1.9, the name will be 'EChoiceField'.
By default for Django >= 1.9, the name will be the name of the enum appended with 'Field'.
kwargs
Passed to the derived `models.Field`
Returns
-------
EChoiceField
For Django>=1.9, the exact name of the returned Field is based on the name of the `echoices` with a suffixed
'Field'. For older Django, the returned name of the class is `EChoiceField`.
"""
assert issubclass(echoices, EChoice)
value_type = echoices.__getvaluetype__()
if value_type is str:
cls_ = models.CharField
elif value_type is int:
cls_ = models.IntegerField
elif value_type is float:
cls_ = models.FloatField
elif value_type is bool:
cls_ = models.BooleanField
else:
raise NotImplementedError("Please open an issue if you wish your value type to be supported: "
"https://github.com/mbourqui/django-echoices/issues/new")
if klass_name and StrictVersion(django_version()) < StrictVersion('1.9.0'):
warnings.warn("Django < 1.9 throws an 'ImportError' if the class name is not defined in the module. "
"The provided klass_name will be replaced by {}".format(EChoiceField.__name__), RuntimeWarning)
klass_name = EChoiceField.__name__ if StrictVersion(django_version()) < StrictVersion('1.9.0') else \
klass_name if klass_name else "{}Field".format(echoices.__name__)
d = dict(cls_.__dict__)
d.update(dict(EChoiceField.__dict__))
return type(klass_name, (cls_,), d)(echoices, *args, **kwargs) | python | def make_echoicefield(echoices, *args, klass_name=None, **kwargs):
"""
Construct a subclass of a derived `models.Field` specific to the type of the `EChoice` values.
Parameters
----------
echoices : subclass of EChoice
args
Passed to the derived `models.Field`
klass_name : str
Give a specific name to the returned class.
By default for Django < 1.9, the name will be 'EChoiceField'.
By default for Django >= 1.9, the name will be the name of the enum appended with 'Field'.
kwargs
Passed to the derived `models.Field`
Returns
-------
EChoiceField
For Django>=1.9, the exact name of the returned Field is based on the name of the `echoices` with a suffixed
'Field'. For older Django, the returned name of the class is `EChoiceField`.
"""
assert issubclass(echoices, EChoice)
value_type = echoices.__getvaluetype__()
if value_type is str:
cls_ = models.CharField
elif value_type is int:
cls_ = models.IntegerField
elif value_type is float:
cls_ = models.FloatField
elif value_type is bool:
cls_ = models.BooleanField
else:
raise NotImplementedError("Please open an issue if you wish your value type to be supported: "
"https://github.com/mbourqui/django-echoices/issues/new")
if klass_name and StrictVersion(django_version()) < StrictVersion('1.9.0'):
warnings.warn("Django < 1.9 throws an 'ImportError' if the class name is not defined in the module. "
"The provided klass_name will be replaced by {}".format(EChoiceField.__name__), RuntimeWarning)
klass_name = EChoiceField.__name__ if StrictVersion(django_version()) < StrictVersion('1.9.0') else \
klass_name if klass_name else "{}Field".format(echoices.__name__)
d = dict(cls_.__dict__)
d.update(dict(EChoiceField.__dict__))
return type(klass_name, (cls_,), d)(echoices, *args, **kwargs) | [
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args
Passed to the derived `models.Field`
klass_name : str
Give a specific name to the returned class.
By default for Django < 1.9, the name will be 'EChoiceField'.
By default for Django >= 1.9, the name will be the name of the enum appended with 'Field'.
kwargs
Passed to the derived `models.Field`
Returns
-------
EChoiceField
For Django>=1.9, the exact name of the returned Field is based on the name of the `echoices` with a suffixed
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jstitch/MambuPy | MambuPy/orm/schema_dummies.py | make_dummy | def make_dummy(instance,
relations = {},
datetime_default = dt.strptime('1901-01-01','%Y-%m-%d'),
varchar_default = "",
integer_default = 0,
numeric_default = 0.0,
*args, **kwargs
):
"""Make an instance to look like an empty dummy.
Every field of the table is set with zeroes/empty strings.
Date fields are set to 01/01/1901.
* relations is a dictionary to set properties for relationships
on the instance.
The keys of the relations dictionary are the name of the fields to
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The values of the relations dictionary must be 2 dimension tuples:
- first element will be the element to be related.
- second element will be the name of the backref set on the previous
first element of the tuple, as a list containing the instance.
If you wish that no backref to be set you may use any invalid value
for a property name, anything other than a string, for example a
number. Preferably, use None.
* datetime_default is the datetime object to use for init datetime
fields. Defaults to 01-01-1901
* varchar_default is the string object to use for init varchar
fields. Defaults to ""
* integer_default is the int object to use for init integer
fields. Defaults to 0
* numeric_default is the float object to use for init numeric
fields. Defaults to 0.0
* kwargs may have the name of a certain field you wish to initialize
with a value other than the given by the init_data dicionary. If you
give an unexistent name on the columns of the table, they are safely
ignored.
.. todo:: further field types may be set at the init_data dictionary.
"""
# init_data knows how to put an init value depending on data type
init_data = {
'DATETIME' : datetime_default,
'VARCHAR' : varchar_default,
'INTEGER' : integer_default,
'NUMERIC(50, 10)' : numeric_default,
'TEXT' : varchar_default,
}
# the type of the instance is the SQLAlchemy Table
table = type(instance)
for col in table.__table__.columns:
# declarative base tables have a columns property useful for reflection
try:
setattr(instance, col.name, kwargs[col.name])
except KeyError:
setattr(instance, col.name, init_data[str(col.type)])
for k,v in relations.iteritems():
# set the relationship property with the first element of the tuple
setattr(instance, k, v[0])
# try:
# # set the relationship backref on the first element of the tuple
# # with a property named according to the second element of the
# # tuple, pointing to a list with the instance itself (assumes a
# # one-to-many relationship)
# # in case you don't want a backref, just send a None as v[1]
# try:
# getattr(v[0], v[1]).append(instance)
# except:
# setattr(v[0], v[1], [ instance ])
# except:
# pass
return instance | python | def make_dummy(instance,
relations = {},
datetime_default = dt.strptime('1901-01-01','%Y-%m-%d'),
varchar_default = "",
integer_default = 0,
numeric_default = 0.0,
*args, **kwargs
):
"""Make an instance to look like an empty dummy.
Every field of the table is set with zeroes/empty strings.
Date fields are set to 01/01/1901.
* relations is a dictionary to set properties for relationships
on the instance.
The keys of the relations dictionary are the name of the fields to
be set at the instance.
The values of the relations dictionary must be 2 dimension tuples:
- first element will be the element to be related.
- second element will be the name of the backref set on the previous
first element of the tuple, as a list containing the instance.
If you wish that no backref to be set you may use any invalid value
for a property name, anything other than a string, for example a
number. Preferably, use None.
* datetime_default is the datetime object to use for init datetime
fields. Defaults to 01-01-1901
* varchar_default is the string object to use for init varchar
fields. Defaults to ""
* integer_default is the int object to use for init integer
fields. Defaults to 0
* numeric_default is the float object to use for init numeric
fields. Defaults to 0.0
* kwargs may have the name of a certain field you wish to initialize
with a value other than the given by the init_data dicionary. If you
give an unexistent name on the columns of the table, they are safely
ignored.
.. todo:: further field types may be set at the init_data dictionary.
"""
# init_data knows how to put an init value depending on data type
init_data = {
'DATETIME' : datetime_default,
'VARCHAR' : varchar_default,
'INTEGER' : integer_default,
'NUMERIC(50, 10)' : numeric_default,
'TEXT' : varchar_default,
}
# the type of the instance is the SQLAlchemy Table
table = type(instance)
for col in table.__table__.columns:
# declarative base tables have a columns property useful for reflection
try:
setattr(instance, col.name, kwargs[col.name])
except KeyError:
setattr(instance, col.name, init_data[str(col.type)])
for k,v in relations.iteritems():
# set the relationship property with the first element of the tuple
setattr(instance, k, v[0])
# try:
# # set the relationship backref on the first element of the tuple
# # with a property named according to the second element of the
# # tuple, pointing to a list with the instance itself (assumes a
# # one-to-many relationship)
# # in case you don't want a backref, just send a None as v[1]
# try:
# getattr(v[0], v[1]).append(instance)
# except:
# setattr(v[0], v[1], [ instance ])
# except:
# pass
return instance | [
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The keys of the relations dictionary are the name of the fields to
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* integer_default is the int object to use for init integer
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* numeric_default is the float object to use for init numeric
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] | 2af98cc12e7ed5ec183b3e97644e880e70b79ee8 | https://github.com/jstitch/MambuPy/blob/2af98cc12e7ed5ec183b3e97644e880e70b79ee8/MambuPy/orm/schema_dummies.py#L14-L99 | train |
GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network.set_up_network | def set_up_network(
self,
genes: List[Gene],
gene_filter: bool = False,
disease_associations: Optional[Dict] = None
) -> None:
"""Set up the network.
Filter genes out if requested and add attributes to the vertices.
:param genes: A list of Gene objects.
:param gene_filter: Removes all genes that are not in list <genes> if True.
:param disease_associations: Diseases associated with genes.
"""
if gene_filter:
self.filter_genes([gene.entrez_id for gene in genes])
self._add_vertex_attributes(genes, disease_associations)
self.print_summary("Graph of all genes") | python | def set_up_network(
self,
genes: List[Gene],
gene_filter: bool = False,
disease_associations: Optional[Dict] = None
) -> None:
"""Set up the network.
Filter genes out if requested and add attributes to the vertices.
:param genes: A list of Gene objects.
:param gene_filter: Removes all genes that are not in list <genes> if True.
:param disease_associations: Diseases associated with genes.
"""
if gene_filter:
self.filter_genes([gene.entrez_id for gene in genes])
self._add_vertex_attributes(genes, disease_associations)
self.print_summary("Graph of all genes") | [
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network.filter_genes | def filter_genes(self, relevant_entrez: list) -> None:
"""Filter out the genes that are not in list relevant_entrez.
:param list relevant_entrez: Entrez IDs of genes which are to be kept.
"""
logger.info("In filter_genes()")
irrelevant_genes = self.graph.vs.select(name_notin=relevant_entrez)
self.graph.delete_vertices(irrelevant_genes) | python | def filter_genes(self, relevant_entrez: list) -> None:
"""Filter out the genes that are not in list relevant_entrez.
:param list relevant_entrez: Entrez IDs of genes which are to be kept.
"""
logger.info("In filter_genes()")
irrelevant_genes = self.graph.vs.select(name_notin=relevant_entrez)
self.graph.delete_vertices(irrelevant_genes) | [
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network._add_vertex_attributes | def _add_vertex_attributes(self, genes: List[Gene],
disease_associations: Optional[dict] = None) -> None:
"""Add attributes to vertices.
:param genes: A list of genes containing attribute information.
"""
self._set_default_vertex_attributes()
self._add_vertex_attributes_by_genes(genes)
# compute up-regulated and down-regulated genes
up_regulated = self.get_upregulated_genes()
down_regulated = self.get_downregulated_genes()
# set the attributes for up-regulated and down-regulated genes
self.graph.vs(up_regulated.indices)["diff_expressed"] = True
self.graph.vs(up_regulated.indices)["up_regulated"] = True
self.graph.vs(down_regulated.indices)["diff_expressed"] = True
self.graph.vs(down_regulated.indices)["down_regulated"] = True
# add disease associations
self._add_disease_associations(disease_associations)
logger.info("Number of all differentially expressed genes is: {}".
format(len(up_regulated) + len(down_regulated))) | python | def _add_vertex_attributes(self, genes: List[Gene],
disease_associations: Optional[dict] = None) -> None:
"""Add attributes to vertices.
:param genes: A list of genes containing attribute information.
"""
self._set_default_vertex_attributes()
self._add_vertex_attributes_by_genes(genes)
# compute up-regulated and down-regulated genes
up_regulated = self.get_upregulated_genes()
down_regulated = self.get_downregulated_genes()
# set the attributes for up-regulated and down-regulated genes
self.graph.vs(up_regulated.indices)["diff_expressed"] = True
self.graph.vs(up_regulated.indices)["up_regulated"] = True
self.graph.vs(down_regulated.indices)["diff_expressed"] = True
self.graph.vs(down_regulated.indices)["down_regulated"] = True
# add disease associations
self._add_disease_associations(disease_associations)
logger.info("Number of all differentially expressed genes is: {}".
format(len(up_regulated) + len(down_regulated))) | [
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network._set_default_vertex_attributes | def _set_default_vertex_attributes(self) -> None:
"""Assign default values on attributes to all vertices."""
self.graph.vs["l2fc"] = 0
self.graph.vs["padj"] = 0.5
self.graph.vs["symbol"] = self.graph.vs["name"]
self.graph.vs["diff_expressed"] = False
self.graph.vs["up_regulated"] = False
self.graph.vs["down_regulated"] = False | python | def _set_default_vertex_attributes(self) -> None:
"""Assign default values on attributes to all vertices."""
self.graph.vs["l2fc"] = 0
self.graph.vs["padj"] = 0.5
self.graph.vs["symbol"] = self.graph.vs["name"]
self.graph.vs["diff_expressed"] = False
self.graph.vs["up_regulated"] = False
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network._add_vertex_attributes_by_genes | def _add_vertex_attributes_by_genes(self, genes: List[Gene]) -> None:
"""Assign values to attributes on vertices.
:param genes: A list of Gene objects from which values will be extracted.
"""
for gene in genes:
try:
vertex = self.graph.vs.find(name=str(gene.entrez_id)).index
self.graph.vs[vertex]['l2fc'] = gene.log2_fold_change
self.graph.vs[vertex]['symbol'] = gene.symbol
self.graph.vs[vertex]['padj'] = gene.padj
except ValueError:
pass | python | def _add_vertex_attributes_by_genes(self, genes: List[Gene]) -> None:
"""Assign values to attributes on vertices.
:param genes: A list of Gene objects from which values will be extracted.
"""
for gene in genes:
try:
vertex = self.graph.vs.find(name=str(gene.entrez_id)).index
self.graph.vs[vertex]['l2fc'] = gene.log2_fold_change
self.graph.vs[vertex]['symbol'] = gene.symbol
self.graph.vs[vertex]['padj'] = gene.padj
except ValueError:
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network._add_disease_associations | def _add_disease_associations(self, disease_associations: dict) -> None:
"""Add disease association annotation to the network.
:param disease_associations: Dictionary of disease-gene associations.
"""
if disease_associations is not None:
for target_id, disease_id_list in disease_associations.items():
if target_id in self.graph.vs["name"]:
self.graph.vs.find(name=target_id)["associated_diseases"] = disease_id_list | python | def _add_disease_associations(self, disease_associations: dict) -> None:
"""Add disease association annotation to the network.
:param disease_associations: Dictionary of disease-gene associations.
"""
if disease_associations is not None:
for target_id, disease_id_list in disease_associations.items():
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self.graph.vs.find(name=target_id)["associated_diseases"] = disease_id_list | [
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network.get_upregulated_genes | def get_upregulated_genes(self) -> VertexSeq:
"""Get genes that are up-regulated.
:return: Up-regulated genes.
"""
up_regulated = self.graph.vs.select(self._is_upregulated_gene)
logger.info(f"No. of up-regulated genes after laying on network: {len(up_regulated)}")
return up_regulated | python | def get_upregulated_genes(self) -> VertexSeq:
"""Get genes that are up-regulated.
:return: Up-regulated genes.
"""
up_regulated = self.graph.vs.select(self._is_upregulated_gene)
logger.info(f"No. of up-regulated genes after laying on network: {len(up_regulated)}")
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network.get_downregulated_genes | def get_downregulated_genes(self) -> VertexSeq:
"""Get genes that are down-regulated.
:return: Down-regulated genes.
"""
down_regulated = self.graph.vs.select(self._is_downregulated_gene)
logger.info(f"No. of down-regulated genes after laying on network: {len(down_regulated)}")
return down_regulated | python | def get_downregulated_genes(self) -> VertexSeq:
"""Get genes that are down-regulated.
:return: Down-regulated genes.
"""
down_regulated = self.graph.vs.select(self._is_downregulated_gene)
logger.info(f"No. of down-regulated genes after laying on network: {len(down_regulated)}")
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network.print_summary | def print_summary(self, heading: str) -> None:
"""Print the summary of a graph.
:param str heading: Title of the graph.
"""
logger.info(heading)
logger.info("Number of nodes: {}".format(len(self.graph.vs)))
logger.info("Number of edges: {}".format(len(self.graph.es))) | python | def print_summary(self, heading: str) -> None:
"""Print the summary of a graph.
:param str heading: Title of the graph.
"""
logger.info(heading)
logger.info("Number of nodes: {}".format(len(self.graph.vs)))
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network.get_differentially_expressed_genes | def get_differentially_expressed_genes(self, diff_type: str) -> VertexSeq:
"""Get the differentially expressed genes based on diff_type.
:param str diff_type: Differential expression type chosen by the user; all, down, or up.
:return list: A list of differentially expressed genes.
"""
if diff_type == "up":
diff_expr = self.graph.vs.select(up_regulated_eq=True)
elif diff_type == "down":
diff_expr = self.graph.vs.select(down_regulated_eq=True)
else:
diff_expr = self.graph.vs.select(diff_expressed_eq=True)
return diff_expr | python | def get_differentially_expressed_genes(self, diff_type: str) -> VertexSeq:
"""Get the differentially expressed genes based on diff_type.
:param str diff_type: Differential expression type chosen by the user; all, down, or up.
:return list: A list of differentially expressed genes.
"""
if diff_type == "up":
diff_expr = self.graph.vs.select(up_regulated_eq=True)
elif diff_type == "down":
diff_expr = self.graph.vs.select(down_regulated_eq=True)
else:
diff_expr = self.graph.vs.select(diff_expressed_eq=True)
return diff_expr | [
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network.write_adj_list | def write_adj_list(self, path: str) -> None:
"""Write the network as an adjacency list to a file.
:param path: File path to write the adjacency list.
"""
adj_list = self.get_adjlist()
with open(path, mode="w") as file:
for i, line in enumerate(adj_list):
print(i, *line, file=file) | python | def write_adj_list(self, path: str) -> None:
"""Write the network as an adjacency list to a file.
:param path: File path to write the adjacency list.
"""
adj_list = self.get_adjlist()
with open(path, mode="w") as file:
for i, line in enumerate(adj_list):
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/model/network.py | Network.get_attribute_from_indices | def get_attribute_from_indices(self, indices: list, attribute_name: str):
"""Get attribute values for the requested indices.
:param indices: Indices of vertices for which the attribute values are requested.
:param attribute_name: The name of the attribute.
:return: A list of attribute values for the requested indices.
"""
return list(np.array(self.graph.vs[attribute_name])[indices]) | python | def get_attribute_from_indices(self, indices: list, attribute_name: str):
"""Get attribute values for the requested indices.
:param indices: Indices of vertices for which the attribute values are requested.
:param attribute_name: The name of the attribute.
:return: A list of attribute values for the requested indices.
"""
return list(np.array(self.graph.vs[attribute_name])[indices]) | [
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rsgalloway/grit | grit/server/cherrypy/__init__.py | read_headers | def read_headers(rfile, hdict=None):
"""Read headers from the given stream into the given header dict.
If hdict is None, a new header dict is created. Returns the populated
header dict.
Headers which are repeated are folded together using a comma if their
specification so dictates.
This function raises ValueError when the read bytes violate the HTTP spec.
You should probably return "400 Bad Request" if this happens.
"""
if hdict is None:
hdict = {}
while True:
line = rfile.readline()
if not line:
# No more data--illegal end of headers
raise ValueError("Illegal end of headers.")
if line == CRLF:
# Normal end of headers
break
if not line.endswith(CRLF):
raise ValueError("HTTP requires CRLF terminators")
if line[0] in ' \t':
# It's a continuation line.
v = line.strip()
else:
try:
k, v = line.split(":", 1)
except ValueError:
raise ValueError("Illegal header line.")
# TODO: what about TE and WWW-Authenticate?
k = k.strip().title()
v = v.strip()
hname = k
if k in comma_separated_headers:
existing = hdict.get(hname)
if existing:
v = ", ".join((existing, v))
hdict[hname] = v
return hdict | python | def read_headers(rfile, hdict=None):
"""Read headers from the given stream into the given header dict.
If hdict is None, a new header dict is created. Returns the populated
header dict.
Headers which are repeated are folded together using a comma if their
specification so dictates.
This function raises ValueError when the read bytes violate the HTTP spec.
You should probably return "400 Bad Request" if this happens.
"""
if hdict is None:
hdict = {}
while True:
line = rfile.readline()
if not line:
# No more data--illegal end of headers
raise ValueError("Illegal end of headers.")
if line == CRLF:
# Normal end of headers
break
if not line.endswith(CRLF):
raise ValueError("HTTP requires CRLF terminators")
if line[0] in ' \t':
# It's a continuation line.
v = line.strip()
else:
try:
k, v = line.split(":", 1)
except ValueError:
raise ValueError("Illegal header line.")
# TODO: what about TE and WWW-Authenticate?
k = k.strip().title()
v = v.strip()
hname = k
if k in comma_separated_headers:
existing = hdict.get(hname)
if existing:
v = ", ".join((existing, v))
hdict[hname] = v
return hdict | [
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rsgalloway/grit | grit/server/cherrypy/__init__.py | HTTPRequest.parse_request | def parse_request(self):
"""Parse the next HTTP request start-line and message-headers."""
self.rfile = SizeCheckWrapper(self.conn.rfile,
self.server.max_request_header_size)
try:
self.read_request_line()
except MaxSizeExceeded:
self.simple_response("414 Request-URI Too Long",
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return
try:
success = self.read_request_headers()
except MaxSizeExceeded:
self.simple_response("413 Request Entity Too Large",
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return
else:
if not success:
return
self.ready = True | python | def parse_request(self):
"""Parse the next HTTP request start-line and message-headers."""
self.rfile = SizeCheckWrapper(self.conn.rfile,
self.server.max_request_header_size)
try:
self.read_request_line()
except MaxSizeExceeded:
self.simple_response("414 Request-URI Too Long",
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return
try:
success = self.read_request_headers()
except MaxSizeExceeded:
self.simple_response("413 Request Entity Too Large",
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return
else:
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self.ready = True | [
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rsgalloway/grit | grit/server/cherrypy/__init__.py | HTTPRequest.send_headers | def send_headers(self):
"""Assert, process, and send the HTTP response message-headers.
You must set self.status, and self.outheaders before calling this.
"""
hkeys = [key.lower() for key, value in self.outheaders]
status = int(self.status[:3])
if status == 413:
# Request Entity Too Large. Close conn to avoid garbage.
self.close_connection = True
elif "content-length" not in hkeys:
# "All 1xx (informational), 204 (no content),
# and 304 (not modified) responses MUST NOT
# include a message-body." So no point chunking.
if status < 200 or status in (204, 205, 304):
pass
else:
if (self.response_protocol == 'HTTP/1.1'
and self.method != 'HEAD'):
# Use the chunked transfer-coding
self.chunked_write = True
self.outheaders.append(("Transfer-Encoding", "chunked"))
else:
# Closing the conn is the only way to determine len.
self.close_connection = True
if "connection" not in hkeys:
if self.response_protocol == 'HTTP/1.1':
# Both server and client are HTTP/1.1 or better
if self.close_connection:
self.outheaders.append(("Connection", "close"))
else:
# Server and/or client are HTTP/1.0
if not self.close_connection:
self.outheaders.append(("Connection", "Keep-Alive"))
if (not self.close_connection) and (not self.chunked_read):
# Read any remaining request body data on the socket.
# "If an origin server receives a request that does not include an
# Expect request-header field with the "100-continue" expectation,
# the request includes a request body, and the server responds
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# from the transport connection, then the server SHOULD NOT close
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# or until the client closes the connection. Otherwise, the client
# might not reliably receive the response message. However, this
# requirement is not be construed as preventing a server from
# defending itself against denial-of-service attacks, or from
# badly broken client implementations."
remaining = getattr(self.rfile, 'remaining', 0)
if remaining > 0:
self.rfile.read(remaining)
if "date" not in hkeys:
self.outheaders.append(("Date", rfc822.formatdate()))
if "server" not in hkeys:
self.outheaders.append(("Server", self.server.server_name))
buf = [self.server.protocol + " " + self.status + CRLF]
for k, v in self.outheaders:
buf.append(k + ": " + v + CRLF)
buf.append(CRLF)
self.conn.wfile.sendall("".join(buf)) | python | def send_headers(self):
"""Assert, process, and send the HTTP response message-headers.
You must set self.status, and self.outheaders before calling this.
"""
hkeys = [key.lower() for key, value in self.outheaders]
status = int(self.status[:3])
if status == 413:
# Request Entity Too Large. Close conn to avoid garbage.
self.close_connection = True
elif "content-length" not in hkeys:
# "All 1xx (informational), 204 (no content),
# and 304 (not modified) responses MUST NOT
# include a message-body." So no point chunking.
if status < 200 or status in (204, 205, 304):
pass
else:
if (self.response_protocol == 'HTTP/1.1'
and self.method != 'HEAD'):
# Use the chunked transfer-coding
self.chunked_write = True
self.outheaders.append(("Transfer-Encoding", "chunked"))
else:
# Closing the conn is the only way to determine len.
self.close_connection = True
if "connection" not in hkeys:
if self.response_protocol == 'HTTP/1.1':
# Both server and client are HTTP/1.1 or better
if self.close_connection:
self.outheaders.append(("Connection", "close"))
else:
# Server and/or client are HTTP/1.0
if not self.close_connection:
self.outheaders.append(("Connection", "Keep-Alive"))
if (not self.close_connection) and (not self.chunked_read):
# Read any remaining request body data on the socket.
# "If an origin server receives a request that does not include an
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# might not reliably receive the response message. However, this
# requirement is not be construed as preventing a server from
# defending itself against denial-of-service attacks, or from
# badly broken client implementations."
remaining = getattr(self.rfile, 'remaining', 0)
if remaining > 0:
self.rfile.read(remaining)
if "date" not in hkeys:
self.outheaders.append(("Date", rfc822.formatdate()))
if "server" not in hkeys:
self.outheaders.append(("Server", self.server.server_name))
buf = [self.server.protocol + " " + self.status + CRLF]
for k, v in self.outheaders:
buf.append(k + ": " + v + CRLF)
buf.append(CRLF)
self.conn.wfile.sendall("".join(buf)) | [
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rsgalloway/grit | grit/server/cherrypy/__init__.py | ThreadPool.start | def start(self):
"""Start the pool of threads."""
for i in range(self.min):
self._threads.append(WorkerThread(self.server))
for worker in self._threads:
worker.setName("CP Server " + worker.getName())
worker.start()
for worker in self._threads:
while not worker.ready:
time.sleep(.1) | python | def start(self):
"""Start the pool of threads."""
for i in range(self.min):
self._threads.append(WorkerThread(self.server))
for worker in self._threads:
worker.setName("CP Server " + worker.getName())
worker.start()
for worker in self._threads:
while not worker.ready:
time.sleep(.1) | [
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openvax/varlens | varlens/read_evidence/pileup_element.py | PileupElement.fields | def fields(self):
'''
Fields that should be considered for our notion of object equality.
'''
return (
self.locus, self.offset_start, self.offset_end, self.alignment_key) | python | def fields(self):
'''
Fields that should be considered for our notion of object equality.
'''
return (
self.locus, self.offset_start, self.offset_end, self.alignment_key) | [
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openvax/varlens | varlens/read_evidence/pileup_element.py | PileupElement.bases | def bases(self):
'''
The sequenced bases in the alignment that align to this locus in the
genome, as a string.
Empty string in the case of a deletion. String of length > 1 if there
is an insertion here.
'''
sequence = self.alignment.query_sequence
assert self.offset_end <= len(sequence), \
"End offset=%d > sequence length=%d. CIGAR=%s. SEQUENCE=%s" % (
self.offset_end,
len(sequence),
self.alignment.cigarstring,
sequence)
return sequence[self.offset_start:self.offset_end] | python | def bases(self):
'''
The sequenced bases in the alignment that align to this locus in the
genome, as a string.
Empty string in the case of a deletion. String of length > 1 if there
is an insertion here.
'''
sequence = self.alignment.query_sequence
assert self.offset_end <= len(sequence), \
"End offset=%d > sequence length=%d. CIGAR=%s. SEQUENCE=%s" % (
self.offset_end,
len(sequence),
self.alignment.cigarstring,
sequence)
return sequence[self.offset_start:self.offset_end] | [
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openvax/varlens | varlens/read_evidence/pileup_element.py | PileupElement.min_base_quality | def min_base_quality(self):
'''
The minimum of the base qualities. In the case of a deletion, in which
case there are no bases in this PileupElement, the minimum is taken
over the sequenced bases immediately before and after the deletion.
'''
try:
return min(self.base_qualities)
except ValueError:
# We are mid-deletion. We return the minimum of the adjacent bases.
assert self.offset_start == self.offset_end
adjacent_qualities = [
self.alignment.query_qualities[offset]
for offset in [self.offset_start - 1, self.offset_start]
if 0 <= offset < len(self.alignment.query_qualities)
]
return min(adjacent_qualities) | python | def min_base_quality(self):
'''
The minimum of the base qualities. In the case of a deletion, in which
case there are no bases in this PileupElement, the minimum is taken
over the sequenced bases immediately before and after the deletion.
'''
try:
return min(self.base_qualities)
except ValueError:
# We are mid-deletion. We return the minimum of the adjacent bases.
assert self.offset_start == self.offset_end
adjacent_qualities = [
self.alignment.query_qualities[offset]
for offset in [self.offset_start - 1, self.offset_start]
if 0 <= offset < len(self.alignment.query_qualities)
]
return min(adjacent_qualities) | [
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openvax/varlens | varlens/read_evidence/pileup_element.py | PileupElement.from_pysam_alignment | def from_pysam_alignment(locus, pileup_read):
'''
Factory function to create a new PileupElement from a pysam
`PileupRead`.
Parameters
----------
locus : varcode.Locus
Reference locus for which to construct a PileupElement. Must
include exactly one base.
pileup_read : pysam.calignmentfile.PileupRead
pysam PileupRead instance. Its alignment must overlap the locus.
Returns
----------
PileupElement
'''
assert not pileup_read.is_refskip, (
"Can't create a PileupElement in a refskip (typically an intronic "
"gap in an RNA alignment)")
# Pysam has an `aligned_pairs` method that gives a list of
# (offset, locus) pairs indicating the correspondence between bases in
# the alignment and reference loci. Here we use that to compute
# offset_start and offset_end.
#
# This is slightly tricky in the case of insertions and deletions.
# Here are examples of the desired logic.
#
# Target locus = 1000
#
# (1) Simple case: matching bases.
#
# OFFSET LOCUS
# 0 999
# 1 1000
# 2 1001
#
# DESIRED RESULT: offset_start=1, offset_end=2.
#
#
# (2) A 1 base insertion at offset 2.
#
# OFFSET LOCUS
# 0 999
# 1 1000
# 2 None
# 3 1001
#
# DESIRED RESULT: offset_start = 1, offset_end=3.
#
#
# (3) A 2 base deletion at loci 1000 and 1001.
#
# OFFSET LOCUS
# 0 999
# None 1000
# None 1001
# 1 1002
#
# DESIRED RESULT: offset_start = 1, offset_end=1.
#
offset_start = None
offset_end = len(pileup_read.alignment.query_sequence)
# TODO: doing this with get_blocks() may be faster.
for (offset, position) in pileup_read.alignment.aligned_pairs:
if offset is not None and position is not None:
if position == locus.position:
offset_start = offset
elif position > locus.position:
offset_end = offset
break
if offset_start is None:
offset_start = offset_end
assert pileup_read.is_del == (offset_end - offset_start == 0), \
"Deletion=%s but | [%d,%d) |=%d for locus %d in: \n%s" % (
pileup_read.is_del,
offset_start,
offset_end,
offset_end - offset_start,
locus.position,
pileup_read.alignment.aligned_pairs)
assert offset_end >= offset_start
result = PileupElement(
locus, offset_start, offset_end, pileup_read.alignment)
return result | python | def from_pysam_alignment(locus, pileup_read):
'''
Factory function to create a new PileupElement from a pysam
`PileupRead`.
Parameters
----------
locus : varcode.Locus
Reference locus for which to construct a PileupElement. Must
include exactly one base.
pileup_read : pysam.calignmentfile.PileupRead
pysam PileupRead instance. Its alignment must overlap the locus.
Returns
----------
PileupElement
'''
assert not pileup_read.is_refskip, (
"Can't create a PileupElement in a refskip (typically an intronic "
"gap in an RNA alignment)")
# Pysam has an `aligned_pairs` method that gives a list of
# (offset, locus) pairs indicating the correspondence between bases in
# the alignment and reference loci. Here we use that to compute
# offset_start and offset_end.
#
# This is slightly tricky in the case of insertions and deletions.
# Here are examples of the desired logic.
#
# Target locus = 1000
#
# (1) Simple case: matching bases.
#
# OFFSET LOCUS
# 0 999
# 1 1000
# 2 1001
#
# DESIRED RESULT: offset_start=1, offset_end=2.
#
#
# (2) A 1 base insertion at offset 2.
#
# OFFSET LOCUS
# 0 999
# 1 1000
# 2 None
# 3 1001
#
# DESIRED RESULT: offset_start = 1, offset_end=3.
#
#
# (3) A 2 base deletion at loci 1000 and 1001.
#
# OFFSET LOCUS
# 0 999
# None 1000
# None 1001
# 1 1002
#
# DESIRED RESULT: offset_start = 1, offset_end=1.
#
offset_start = None
offset_end = len(pileup_read.alignment.query_sequence)
# TODO: doing this with get_blocks() may be faster.
for (offset, position) in pileup_read.alignment.aligned_pairs:
if offset is not None and position is not None:
if position == locus.position:
offset_start = offset
elif position > locus.position:
offset_end = offset
break
if offset_start is None:
offset_start = offset_end
assert pileup_read.is_del == (offset_end - offset_start == 0), \
"Deletion=%s but | [%d,%d) |=%d for locus %d in: \n%s" % (
pileup_read.is_del,
offset_start,
offset_end,
offset_end - offset_start,
locus.position,
pileup_read.alignment.aligned_pairs)
assert offset_end >= offset_start
result = PileupElement(
locus, offset_start, offset_end, pileup_read.alignment)
return result | [
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locus : varcode.Locus
Reference locus for which to construct a PileupElement. Must
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pileup_read : pysam.calignmentfile.PileupRead
pysam PileupRead instance. Its alignment must overlap the locus.
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polyaxon/hestia | hestia/http.py | safe_request | def safe_request(
url,
method=None,
params=None,
data=None,
json=None,
headers=None,
allow_redirects=False,
timeout=30,
verify_ssl=True,
):
"""A slightly safer version of `request`."""
session = requests.Session()
kwargs = {}
if json:
kwargs['json'] = json
if not headers:
headers = {}
headers.setdefault('Content-Type', 'application/json')
if data:
kwargs['data'] = data
if params:
kwargs['params'] = params
if headers:
kwargs['headers'] = headers
if method is None:
method = 'POST' if (data or json) else 'GET'
response = session.request(
method=method,
url=url,
allow_redirects=allow_redirects,
timeout=timeout,
verify=verify_ssl,
**kwargs
)
return response | python | def safe_request(
url,
method=None,
params=None,
data=None,
json=None,
headers=None,
allow_redirects=False,
timeout=30,
verify_ssl=True,
):
"""A slightly safer version of `request`."""
session = requests.Session()
kwargs = {}
if json:
kwargs['json'] = json
if not headers:
headers = {}
headers.setdefault('Content-Type', 'application/json')
if data:
kwargs['data'] = data
if params:
kwargs['params'] = params
if headers:
kwargs['headers'] = headers
if method is None:
method = 'POST' if (data or json) else 'GET'
response = session.request(
method=method,
url=url,
allow_redirects=allow_redirects,
timeout=timeout,
verify=verify_ssl,
**kwargs
)
return response | [
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klmitch/turnstile | turnstile/remote.py | remote | def remote(func):
"""
Decorator to mark a function as invoking a remote procedure call.
When invoked in server mode, the function will be called; when
invoked in client mode, an RPC will be initiated.
"""
@functools.wraps(func)
def wrapper(self, *args, **kwargs):
if self.mode == 'server':
# In server mode, call the function
return func(self, *args, **kwargs)
# Make sure we're connected
if not self.conn:
self.connect()
# Call the remote function
self.conn.send('CALL', func.__name__, args, kwargs)
# Receive the response
cmd, payload = self.conn.recv()
if cmd == 'ERR':
self.close()
raise Exception("Catastrophic error from server: %s" %
payload[0])
elif cmd == 'EXC':
exc_type = utils.find_entrypoint(None, payload[0])
raise exc_type(payload[1])
elif cmd != 'RES':
self.close()
raise Exception("Invalid command response from server: %s" % cmd)
return payload[0]
# Mark it a callable
wrapper._remote = True
# Return the wrapped function
return wrapper | python | def remote(func):
"""
Decorator to mark a function as invoking a remote procedure call.
When invoked in server mode, the function will be called; when
invoked in client mode, an RPC will be initiated.
"""
@functools.wraps(func)
def wrapper(self, *args, **kwargs):
if self.mode == 'server':
# In server mode, call the function
return func(self, *args, **kwargs)
# Make sure we're connected
if not self.conn:
self.connect()
# Call the remote function
self.conn.send('CALL', func.__name__, args, kwargs)
# Receive the response
cmd, payload = self.conn.recv()
if cmd == 'ERR':
self.close()
raise Exception("Catastrophic error from server: %s" %
payload[0])
elif cmd == 'EXC':
exc_type = utils.find_entrypoint(None, payload[0])
raise exc_type(payload[1])
elif cmd != 'RES':
self.close()
raise Exception("Invalid command response from server: %s" % cmd)
return payload[0]
# Mark it a callable
wrapper._remote = True
# Return the wrapped function
return wrapper | [
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klmitch/turnstile | turnstile/remote.py | Connection.send | def send(self, cmd, *payload):
"""
Send a command message to the other end.
:param cmd: The command to send to the other end.
:param payload: The command payload. Note that all elements
of the payload must be serializable to JSON.
"""
# If it's closed, raise an error up front
if not self._sock:
raise ConnectionClosed("Connection closed")
# Construct the outgoing message
msg = json.dumps(dict(cmd=cmd, payload=payload)) + '\n'
# Send it
try:
self._sock.sendall(msg)
except socket.error:
# We'll need to re-raise
e_type, e_value, e_tb = sys.exc_info()
# Make sure the socket is closed
self.close()
# Re-raise
raise e_type, e_value, e_tb | python | def send(self, cmd, *payload):
"""
Send a command message to the other end.
:param cmd: The command to send to the other end.
:param payload: The command payload. Note that all elements
of the payload must be serializable to JSON.
"""
# If it's closed, raise an error up front
if not self._sock:
raise ConnectionClosed("Connection closed")
# Construct the outgoing message
msg = json.dumps(dict(cmd=cmd, payload=payload)) + '\n'
# Send it
try:
self._sock.sendall(msg)
except socket.error:
# We'll need to re-raise
e_type, e_value, e_tb = sys.exc_info()
# Make sure the socket is closed
self.close()
# Re-raise
raise e_type, e_value, e_tb | [
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klmitch/turnstile | turnstile/remote.py | Connection._recvbuf_pop | def _recvbuf_pop(self):
"""
Internal helper to pop a message off the receive buffer. If
the message is an Exception, that exception will be raised;
otherwise, a tuple of command and payload will be returned.
"""
# Pop a message off the recv buffer and return (or raise) it
msg = self._recvbuf.pop(0)
if isinstance(msg, Exception):
raise msg
return msg['cmd'], msg['payload'] | python | def _recvbuf_pop(self):
"""
Internal helper to pop a message off the receive buffer. If
the message is an Exception, that exception will be raised;
otherwise, a tuple of command and payload will be returned.
"""
# Pop a message off the recv buffer and return (or raise) it
msg = self._recvbuf.pop(0)
if isinstance(msg, Exception):
raise msg
return msg['cmd'], msg['payload'] | [
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klmitch/turnstile | turnstile/remote.py | SimpleRPC.ping | def ping(self):
"""
Ping the server. Returns the time interval, in seconds,
required for the server to respond to the PING message.
"""
# Make sure we're connected
if not self.conn:
self.connect()
# Send the ping and wait for the response
self.conn.send('PING', time.time())
cmd, payload = self.conn.recv()
recv_ts = time.time()
# Make sure the response was a PONG
if cmd != 'PONG':
raise Exception("Invalid response from server")
# Return the RTT
return recv_ts - payload[0] | python | def ping(self):
"""
Ping the server. Returns the time interval, in seconds,
required for the server to respond to the PING message.
"""
# Make sure we're connected
if not self.conn:
self.connect()
# Send the ping and wait for the response
self.conn.send('PING', time.time())
cmd, payload = self.conn.recv()
recv_ts = time.time()
# Make sure the response was a PONG
if cmd != 'PONG':
raise Exception("Invalid response from server")
# Return the RTT
return recv_ts - payload[0] | [
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klmitch/turnstile | turnstile/remote.py | SimpleRPC.listen | def listen(self):
"""
Listen for clients. This method causes the SimpleRPC object
to switch to server mode. One thread will be created for each
client.
"""
# Make sure we're in server mode
if self.mode and self.mode != 'server':
raise ValueError("%s is not in server mode" %
self.__class__.__name__)
self.mode = 'server'
# Obtain a listening socket
serv = _create_server(self.host, self.port)
# If we have too many errors, we want to bail out
err_thresh = 0
while True:
# Accept a connection
try:
sock, addr = serv.accept()
except Exception as exc:
err_thresh += 1
if err_thresh >= self.max_err_thresh:
LOG.exception("Too many errors accepting "
"connections: %s" % str(exc))
break
continue # Pragma: nocover
# Decrement error count on successful connections
err_thresh = max(err_thresh - 1, 0)
# Log the connection attempt
LOG.info("Accepted connection from %s port %s" %
(addr[0], addr[1]))
# And handle the connection
eventlet.spawn_n(self.serve, self.connection_class(sock), addr)
# Close the listening socket
with utils.ignore_except():
serv.close() | python | def listen(self):
"""
Listen for clients. This method causes the SimpleRPC object
to switch to server mode. One thread will be created for each
client.
"""
# Make sure we're in server mode
if self.mode and self.mode != 'server':
raise ValueError("%s is not in server mode" %
self.__class__.__name__)
self.mode = 'server'
# Obtain a listening socket
serv = _create_server(self.host, self.port)
# If we have too many errors, we want to bail out
err_thresh = 0
while True:
# Accept a connection
try:
sock, addr = serv.accept()
except Exception as exc:
err_thresh += 1
if err_thresh >= self.max_err_thresh:
LOG.exception("Too many errors accepting "
"connections: %s" % str(exc))
break
continue # Pragma: nocover
# Decrement error count on successful connections
err_thresh = max(err_thresh - 1, 0)
# Log the connection attempt
LOG.info("Accepted connection from %s port %s" %
(addr[0], addr[1]))
# And handle the connection
eventlet.spawn_n(self.serve, self.connection_class(sock), addr)
# Close the listening socket
with utils.ignore_except():
serv.close() | [
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klmitch/turnstile | turnstile/remote.py | SimpleRPC.serve | def serve(self, conn, addr, auth=False):
"""
Handle a single client.
:param conn: The Connection instance.
:param addr: The address of the client, for logging purposes.
:param auth: A boolean specifying whether the connection
should be considered authenticated or not.
Provided for debugging.
"""
try:
# Handle data from the client
while True:
# Get the command
try:
cmd, payload = conn.recv()
except ValueError as exc:
# Tell the client about the error
conn.send('ERR', "Failed to parse command: %s" % str(exc))
# If they haven't successfully authenticated yet,
# disconnect them
if not auth:
return
continue # Pragma: nocover
# Log the command and payload, for debugging purposes
LOG.debug("Received command %r from %s port %s; payload: %r" %
(cmd, addr[0], addr[1], payload))
# Handle authentication
if cmd == 'AUTH':
if auth:
conn.send('ERR', "Already authenticated")
elif payload[0] != self.authkey:
# Don't give them a second chance
conn.send('ERR', "Invalid authentication key")
return
else:
# Authentication successful
conn.send('OK')
auth = True
# Handle unauthenticated connections
elif not auth:
# No second chances
conn.send('ERR', "Not authenticated")
return
# Handle aliveness test
elif cmd == 'PING':
conn.send('PONG', *payload)
# Handle a function call command
elif cmd == 'CALL':
try:
# Get the call parameters
try:
funcname, args, kwargs = payload
except ValueError as exc:
conn.send('ERR', "Invalid payload for 'CALL' "
"command: %s" % str(exc))
continue
# Look up the function
func = self._get_remote_method(funcname)
# Call the function
result = func(*args, **kwargs)
except Exception as exc:
exc_name = '%s:%s' % (exc.__class__.__module__,
exc.__class__.__name__)
conn.send('EXC', exc_name, str(exc))
else:
# Return the result
conn.send('RES', result)
# Handle all other commands by returning an ERR
else:
conn.send('ERR', "Unrecognized command %r" % cmd)
except ConnectionClosed:
# Ignore the connection closed error
pass
except Exception as exc:
# Log other exceptions
LOG.exception("Error serving client at %s port %s: %s" %
(addr[0], addr[1], str(exc)))
finally:
LOG.info("Closing connection from %s port %s" %
(addr[0], addr[1]))
# Make sure the socket gets closed
conn.close() | python | def serve(self, conn, addr, auth=False):
"""
Handle a single client.
:param conn: The Connection instance.
:param addr: The address of the client, for logging purposes.
:param auth: A boolean specifying whether the connection
should be considered authenticated or not.
Provided for debugging.
"""
try:
# Handle data from the client
while True:
# Get the command
try:
cmd, payload = conn.recv()
except ValueError as exc:
# Tell the client about the error
conn.send('ERR', "Failed to parse command: %s" % str(exc))
# If they haven't successfully authenticated yet,
# disconnect them
if not auth:
return
continue # Pragma: nocover
# Log the command and payload, for debugging purposes
LOG.debug("Received command %r from %s port %s; payload: %r" %
(cmd, addr[0], addr[1], payload))
# Handle authentication
if cmd == 'AUTH':
if auth:
conn.send('ERR', "Already authenticated")
elif payload[0] != self.authkey:
# Don't give them a second chance
conn.send('ERR', "Invalid authentication key")
return
else:
# Authentication successful
conn.send('OK')
auth = True
# Handle unauthenticated connections
elif not auth:
# No second chances
conn.send('ERR', "Not authenticated")
return
# Handle aliveness test
elif cmd == 'PING':
conn.send('PONG', *payload)
# Handle a function call command
elif cmd == 'CALL':
try:
# Get the call parameters
try:
funcname, args, kwargs = payload
except ValueError as exc:
conn.send('ERR', "Invalid payload for 'CALL' "
"command: %s" % str(exc))
continue
# Look up the function
func = self._get_remote_method(funcname)
# Call the function
result = func(*args, **kwargs)
except Exception as exc:
exc_name = '%s:%s' % (exc.__class__.__module__,
exc.__class__.__name__)
conn.send('EXC', exc_name, str(exc))
else:
# Return the result
conn.send('RES', result)
# Handle all other commands by returning an ERR
else:
conn.send('ERR', "Unrecognized command %r" % cmd)
except ConnectionClosed:
# Ignore the connection closed error
pass
except Exception as exc:
# Log other exceptions
LOG.exception("Error serving client at %s port %s: %s" %
(addr[0], addr[1], str(exc)))
finally:
LOG.info("Closing connection from %s port %s" %
(addr[0], addr[1]))
# Make sure the socket gets closed
conn.close() | [
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:param conn: The Connection instance.
:param addr: The address of the client, for logging purposes.
:param auth: A boolean specifying whether the connection
should be considered authenticated or not.
Provided for debugging. | [
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klmitch/turnstile | turnstile/remote.py | RemoteControlDaemon.get_limits | def get_limits(self):
"""
Retrieve the LimitData object the middleware will use for
getting the limits. This implementation returns a
RemoteLimitData instance that can access the LimitData stored
in the RemoteControlDaemon process.
"""
# Set one up if we don't already have it
if not self.remote_limits:
self.remote_limits = RemoteLimitData(self.remote)
return self.remote_limits | python | def get_limits(self):
"""
Retrieve the LimitData object the middleware will use for
getting the limits. This implementation returns a
RemoteLimitData instance that can access the LimitData stored
in the RemoteControlDaemon process.
"""
# Set one up if we don't already have it
if not self.remote_limits:
self.remote_limits = RemoteLimitData(self.remote)
return self.remote_limits | [
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kata198/python-subprocess2 | subprocess2/__init__.py | waitUpTo | def waitUpTo(self, timeoutSeconds, pollInterval=DEFAULT_POLL_INTERVAL):
'''
Popen.waitUpTo - Wait up to a certain number of seconds for the process to end.
@param timeoutSeconds <float> - Number of seconds to wait
@param pollInterval <float> (default .05) - Number of seconds in between each poll
@return - Returncode of application, or None if did not terminate.
'''
i = 0
numWaits = timeoutSeconds / float(pollInterval)
ret = self.poll()
if ret is None:
while i < numWaits:
time.sleep(pollInterval)
ret = self.poll()
if ret is not None:
break
i += 1
return ret | python | def waitUpTo(self, timeoutSeconds, pollInterval=DEFAULT_POLL_INTERVAL):
'''
Popen.waitUpTo - Wait up to a certain number of seconds for the process to end.
@param timeoutSeconds <float> - Number of seconds to wait
@param pollInterval <float> (default .05) - Number of seconds in between each poll
@return - Returncode of application, or None if did not terminate.
'''
i = 0
numWaits = timeoutSeconds / float(pollInterval)
ret = self.poll()
if ret is None:
while i < numWaits:
time.sleep(pollInterval)
ret = self.poll()
if ret is not None:
break
i += 1
return ret | [
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@param timeoutSeconds <float> - Number of seconds to wait
@param pollInterval <float> (default .05) - Number of seconds in between each poll
@return - Returncode of application, or None if did not terminate. | [
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kata198/python-subprocess2 | subprocess2/__init__.py | waitOrTerminate | def waitOrTerminate(self, timeoutSeconds, pollInterval=DEFAULT_POLL_INTERVAL, terminateToKillSeconds=SUBPROCESS2_DEFAULT_TERMINATE_TO_KILL_SECONDS):
'''
waitOrTerminate - Wait up to a certain number of seconds for the process to end.
If the process is running after the timeout has been exceeded, a SIGTERM will be sent.
Optionally, an additional SIGKILL can be sent after some configurable interval. See #terminateToKillSeconds doc below
@param timeoutSeconds <float> - Number of seconds to wait
@param pollInterval <float> (default .05)- Number of seconds between each poll
@param terminateToKillSeconds <float/None> (default 1.5) - If application does not end before #timeoutSeconds , terminate() will be called.
* If this is set to None, an additional #pollInterval sleep will occur after calling .terminate, to allow the application to cleanup. returnCode will be return of app if finished, or None if did not complete.
* If this is set to 0, no terminate signal will be sent, but directly to kill. Because the application cannot trap this, returnCode will be None.
* If this is set to > 0, that number of seconds maximum will be given between .terminate and .kill. If the application does not terminate before KILL, returnCode will be None.
Windows Note -- On windows SIGTERM and SIGKILL are the same thing.
@return dict { 'returnCode' : <int or None> , 'actionTaken' : <int mask of SUBPROCESS2_PROCESS_*> }
Returns a dict representing results:
"returnCode" matches return of application, or None per #terminateToKillSeconds doc above.
"actionTaken" is a mask of the SUBPROCESS2_PROCESS_* variables. If app completed normally, it will be SUBPROCESS2_PROCESS_COMPLETED, otherwise some mask of SUBPROCESS2_PROCESS_TERMINATED and/or SUBPROCESS2_PROCESS_KILLED
'''
returnCode = self.waitUpTo(timeoutSeconds, pollInterval)
actionTaken = SUBPROCESS2_PROCESS_COMPLETED
if returnCode is None:
if terminateToKillSeconds is None:
self.terminate()
actionTaken |= SUBPROCESS2_PROCESS_TERMINATED
time.sleep(pollInterval) # Give a chance to cleanup
returnCode = self.poll()
elif terminateToKillSeconds == 0:
self.kill()
actionTaken |= SUBPROCESS2_PROCESS_KILLED
time.sleep(.01) # Give a chance to happen
self.poll() # Don't defunct
returnCode = None
else:
self.terminate()
actionTaken |= SUBPROCESS2_PROCESS_TERMINATED
returnCode = self.waitUpTo(terminateToKillSeconds, pollInterval)
if returnCode is None:
actionTaken |= SUBPROCESS2_PROCESS_KILLED
self.kill()
time.sleep(.01)
self.poll() # Don't defunct
return {
'returnCode' : returnCode,
'actionTaken' : actionTaken
} | python | def waitOrTerminate(self, timeoutSeconds, pollInterval=DEFAULT_POLL_INTERVAL, terminateToKillSeconds=SUBPROCESS2_DEFAULT_TERMINATE_TO_KILL_SECONDS):
'''
waitOrTerminate - Wait up to a certain number of seconds for the process to end.
If the process is running after the timeout has been exceeded, a SIGTERM will be sent.
Optionally, an additional SIGKILL can be sent after some configurable interval. See #terminateToKillSeconds doc below
@param timeoutSeconds <float> - Number of seconds to wait
@param pollInterval <float> (default .05)- Number of seconds between each poll
@param terminateToKillSeconds <float/None> (default 1.5) - If application does not end before #timeoutSeconds , terminate() will be called.
* If this is set to None, an additional #pollInterval sleep will occur after calling .terminate, to allow the application to cleanup. returnCode will be return of app if finished, or None if did not complete.
* If this is set to 0, no terminate signal will be sent, but directly to kill. Because the application cannot trap this, returnCode will be None.
* If this is set to > 0, that number of seconds maximum will be given between .terminate and .kill. If the application does not terminate before KILL, returnCode will be None.
Windows Note -- On windows SIGTERM and SIGKILL are the same thing.
@return dict { 'returnCode' : <int or None> , 'actionTaken' : <int mask of SUBPROCESS2_PROCESS_*> }
Returns a dict representing results:
"returnCode" matches return of application, or None per #terminateToKillSeconds doc above.
"actionTaken" is a mask of the SUBPROCESS2_PROCESS_* variables. If app completed normally, it will be SUBPROCESS2_PROCESS_COMPLETED, otherwise some mask of SUBPROCESS2_PROCESS_TERMINATED and/or SUBPROCESS2_PROCESS_KILLED
'''
returnCode = self.waitUpTo(timeoutSeconds, pollInterval)
actionTaken = SUBPROCESS2_PROCESS_COMPLETED
if returnCode is None:
if terminateToKillSeconds is None:
self.terminate()
actionTaken |= SUBPROCESS2_PROCESS_TERMINATED
time.sleep(pollInterval) # Give a chance to cleanup
returnCode = self.poll()
elif terminateToKillSeconds == 0:
self.kill()
actionTaken |= SUBPROCESS2_PROCESS_KILLED
time.sleep(.01) # Give a chance to happen
self.poll() # Don't defunct
returnCode = None
else:
self.terminate()
actionTaken |= SUBPROCESS2_PROCESS_TERMINATED
returnCode = self.waitUpTo(terminateToKillSeconds, pollInterval)
if returnCode is None:
actionTaken |= SUBPROCESS2_PROCESS_KILLED
self.kill()
time.sleep(.01)
self.poll() # Don't defunct
return {
'returnCode' : returnCode,
'actionTaken' : actionTaken
} | [
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If the process is running after the timeout has been exceeded, a SIGTERM will be sent.
Optionally, an additional SIGKILL can be sent after some configurable interval. See #terminateToKillSeconds doc below
@param timeoutSeconds <float> - Number of seconds to wait
@param pollInterval <float> (default .05)- Number of seconds between each poll
@param terminateToKillSeconds <float/None> (default 1.5) - If application does not end before #timeoutSeconds , terminate() will be called.
* If this is set to None, an additional #pollInterval sleep will occur after calling .terminate, to allow the application to cleanup. returnCode will be return of app if finished, or None if did not complete.
* If this is set to 0, no terminate signal will be sent, but directly to kill. Because the application cannot trap this, returnCode will be None.
* If this is set to > 0, that number of seconds maximum will be given between .terminate and .kill. If the application does not terminate before KILL, returnCode will be None.
Windows Note -- On windows SIGTERM and SIGKILL are the same thing.
@return dict { 'returnCode' : <int or None> , 'actionTaken' : <int mask of SUBPROCESS2_PROCESS_*> }
Returns a dict representing results:
"returnCode" matches return of application, or None per #terminateToKillSeconds doc above.
"actionTaken" is a mask of the SUBPROCESS2_PROCESS_* variables. If app completed normally, it will be SUBPROCESS2_PROCESS_COMPLETED, otherwise some mask of SUBPROCESS2_PROCESS_TERMINATED and/or SUBPROCESS2_PROCESS_KILLED | [
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kata198/python-subprocess2 | subprocess2/__init__.py | runInBackground | def runInBackground(self, pollInterval=.1, encoding=False):
'''
runInBackground - Create a background thread which will manage this process, automatically read from streams, and perform any cleanups
The object returned is a "BackgroundTaskInfo" object, and represents the state of the process. It is updated automatically as the program runs,
and if stdout or stderr are streams, they are automatically read from and populated into this object.
@see BackgroundTaskInfo for more info or http://pythonhosted.org/python-subprocess2/subprocess2.BackgroundTask.html
@param pollInterval - Amount of idle time between polling
@param encoding - Default False. If provided, data will be decoded using the value of this field as the codec name (e.x. "utf-8"). Otherwise, data will be stored as bytes.
'''
from .BackgroundTask import BackgroundTaskThread
taskInfo = BackgroundTaskInfo(encoding)
thread = BackgroundTaskThread(self, taskInfo, pollInterval, encoding)
thread.start()
#thread.run() # Uncomment to use pdb debug (will not run in background)
return taskInfo | python | def runInBackground(self, pollInterval=.1, encoding=False):
'''
runInBackground - Create a background thread which will manage this process, automatically read from streams, and perform any cleanups
The object returned is a "BackgroundTaskInfo" object, and represents the state of the process. It is updated automatically as the program runs,
and if stdout or stderr are streams, they are automatically read from and populated into this object.
@see BackgroundTaskInfo for more info or http://pythonhosted.org/python-subprocess2/subprocess2.BackgroundTask.html
@param pollInterval - Amount of idle time between polling
@param encoding - Default False. If provided, data will be decoded using the value of this field as the codec name (e.x. "utf-8"). Otherwise, data will be stored as bytes.
'''
from .BackgroundTask import BackgroundTaskThread
taskInfo = BackgroundTaskInfo(encoding)
thread = BackgroundTaskThread(self, taskInfo, pollInterval, encoding)
thread.start()
#thread.run() # Uncomment to use pdb debug (will not run in background)
return taskInfo | [
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jstitch/MambuPy | MambuPy/rest/mambugroup.py | MambuGroup.setClients | def setClients(self, *args, **kwargs):
"""Adds the clients for this group to a 'clients' field.
The 'groupMembers' field of the group holds the encodedKeys of
the member clients of the group. Since Mambu REST API accepts
both ids or encodedKeys to retrieve entities, we use that here.
You may wish to get the full details of each client by passing a
fullDetails=True argument here.
Returns the number of requests done to Mambu.
"""
requests = 0
if 'fullDetails' in kwargs:
fullDetails = kwargs['fullDetails']
kwargs.pop('fullDetails')
else:
fullDetails = True
clients = []
for m in self['groupMembers']:
try:
client = self.mambuclientclass(entid=m['clientKey'], fullDetails=fullDetails, *args, **kwargs)
except AttributeError as ae:
from .mambuclient import MambuClient
self.mambuclientclass = MambuClient
client = self.mambuclientclass(entid=m['clientKey'], fullDetails=fullDetails, *args, **kwargs)
requests += 1
clients.append(client)
self['clients'] = clients
return requests | python | def setClients(self, *args, **kwargs):
"""Adds the clients for this group to a 'clients' field.
The 'groupMembers' field of the group holds the encodedKeys of
the member clients of the group. Since Mambu REST API accepts
both ids or encodedKeys to retrieve entities, we use that here.
You may wish to get the full details of each client by passing a
fullDetails=True argument here.
Returns the number of requests done to Mambu.
"""
requests = 0
if 'fullDetails' in kwargs:
fullDetails = kwargs['fullDetails']
kwargs.pop('fullDetails')
else:
fullDetails = True
clients = []
for m in self['groupMembers']:
try:
client = self.mambuclientclass(entid=m['clientKey'], fullDetails=fullDetails, *args, **kwargs)
except AttributeError as ae:
from .mambuclient import MambuClient
self.mambuclientclass = MambuClient
client = self.mambuclientclass(entid=m['clientKey'], fullDetails=fullDetails, *args, **kwargs)
requests += 1
clients.append(client)
self['clients'] = clients
return requests | [
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The 'groupMembers' field of the group holds the encodedKeys of
the member clients of the group. Since Mambu REST API accepts
both ids or encodedKeys to retrieve entities, we use that here.
You may wish to get the full details of each client by passing a
fullDetails=True argument here.
Returns the number of requests done to Mambu. | [
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jstitch/MambuPy | MambuPy/rest/mambugroup.py | MambuGroup.setActivities | def setActivities(self, *args, **kwargs):
"""Adds the activities for this group to a 'activities' field.
Activities are MambuActivity objects.
Activities get sorted by activity timestamp.
Returns the number of requests done to Mambu.
"""
def activityDate(activity):
"""Util function used for sorting activities according to timestamp"""
try:
return activity['activity']['timestamp']
except KeyError as kerr:
return None
try:
activities = self.mambuactivitiesclass(groupId=self['encodedKey'], *args, **kwargs)
except AttributeError as ae:
from .mambuactivity import MambuActivities
self.mambuactivitiesclass = MambuActivities
activities = self.mambuactivitiesclass(groupId=self['encodedKey'], *args, **kwargs)
activities.attrs = sorted(activities.attrs, key=activityDate)
self['activities'] = activities
return 1 | python | def setActivities(self, *args, **kwargs):
"""Adds the activities for this group to a 'activities' field.
Activities are MambuActivity objects.
Activities get sorted by activity timestamp.
Returns the number of requests done to Mambu.
"""
def activityDate(activity):
"""Util function used for sorting activities according to timestamp"""
try:
return activity['activity']['timestamp']
except KeyError as kerr:
return None
try:
activities = self.mambuactivitiesclass(groupId=self['encodedKey'], *args, **kwargs)
except AttributeError as ae:
from .mambuactivity import MambuActivities
self.mambuactivitiesclass = MambuActivities
activities = self.mambuactivitiesclass(groupId=self['encodedKey'], *args, **kwargs)
activities.attrs = sorted(activities.attrs, key=activityDate)
self['activities'] = activities
return 1 | [
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azogue/i2csense | i2csense/bh1750.py | BH1750.set_sensitivity | def set_sensitivity(self, sensitivity=DEFAULT_SENSITIVITY):
"""Set the sensitivity value.
Valid values are 31 (lowest) to 254 (highest), default is 69.
"""
if sensitivity < 31:
self._mtreg = 31
elif sensitivity > 254:
self._mtreg = 254
else:
self._mtreg = sensitivity
self._power_on()
self._set_mode(0x40 | (self._mtreg >> 5))
self._set_mode(0x60 | (self._mtreg & 0x1f))
self._power_down() | python | def set_sensitivity(self, sensitivity=DEFAULT_SENSITIVITY):
"""Set the sensitivity value.
Valid values are 31 (lowest) to 254 (highest), default is 69.
"""
if sensitivity < 31:
self._mtreg = 31
elif sensitivity > 254:
self._mtreg = 254
else:
self._mtreg = sensitivity
self._power_on()
self._set_mode(0x40 | (self._mtreg >> 5))
self._set_mode(0x60 | (self._mtreg & 0x1f))
self._power_down() | [
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azogue/i2csense | i2csense/bh1750.py | BH1750._get_result | def _get_result(self) -> float:
"""Return current measurement result in lx."""
try:
data = self._bus.read_word_data(self._i2c_add, self._mode)
self._ok = True
except OSError as exc:
self.log_error("Bad reading in bus: %s", exc)
self._ok = False
return -1
count = data >> 8 | (data & 0xff) << 8
mode2coeff = 2 if self._high_res else 1
ratio = 1 / (1.2 * (self._mtreg / 69.0) * mode2coeff)
return ratio * count | python | def _get_result(self) -> float:
"""Return current measurement result in lx."""
try:
data = self._bus.read_word_data(self._i2c_add, self._mode)
self._ok = True
except OSError as exc:
self.log_error("Bad reading in bus: %s", exc)
self._ok = False
return -1
count = data >> 8 | (data & 0xff) << 8
mode2coeff = 2 if self._high_res else 1
ratio = 1 / (1.2 * (self._mtreg / 69.0) * mode2coeff)
return ratio * count | [
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azogue/i2csense | i2csense/bh1750.py | BH1750._wait_for_result | def _wait_for_result(self):
"""Wait for the sensor to be ready for measurement."""
basetime = 0.018 if self._low_res else 0.128
sleep(basetime * (self._mtreg / 69.0) + self._delay) | python | def _wait_for_result(self):
"""Wait for the sensor to be ready for measurement."""
basetime = 0.018 if self._low_res else 0.128
sleep(basetime * (self._mtreg / 69.0) + self._delay) | [
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azogue/i2csense | i2csense/bh1750.py | BH1750.update | def update(self):
"""Update the measured light level in lux."""
if not self._continuous_sampling \
or self._light_level < 0 \
or self._operation_mode != self._mode:
self._reset()
self._set_mode(self._operation_mode)
self._wait_for_result()
self._light_level = self._get_result()
if not self._continuous_sampling:
self._power_down() | python | def update(self):
"""Update the measured light level in lux."""
if not self._continuous_sampling \
or self._light_level < 0 \
or self._operation_mode != self._mode:
self._reset()
self._set_mode(self._operation_mode)
self._wait_for_result()
self._light_level = self._get_result()
if not self._continuous_sampling:
self._power_down() | [
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jpscaletti/authcode | authcode/utils.py | get_token | def get_token(user, secret, timestamp=None):
"""Make a timestamped one-time-use token that can be used to
identifying the user.
By hashing the `last_sign_in` attribute and a snippet of the current
password hash salt, it produces a token that will be invalidated as soon
as the user log in again or the is changed.
A hash of the user ID is used, so the HMAC part of the token is always
unique for each user.
It also hash a secret key, so without access to the source code,
fake tokens cannot be generated even if the database is compromised.
"""
timestamp = int(timestamp or time())
secret = to_bytes(secret)
key = '|'.join([
hashlib.sha1(secret).hexdigest(),
str(user.id),
get_hash_extract(user.password),
str(getattr(user, 'last_sign_in', 0)),
str(timestamp),
])
key = key.encode('utf8', 'ignore')
mac = hmac.new(key, msg=None, digestmod=hashlib.sha512)
mac = mac.hexdigest()[:50]
token = '{0}${1}${2}'.format(user.id, to36(timestamp), mac)
return token | python | def get_token(user, secret, timestamp=None):
"""Make a timestamped one-time-use token that can be used to
identifying the user.
By hashing the `last_sign_in` attribute and a snippet of the current
password hash salt, it produces a token that will be invalidated as soon
as the user log in again or the is changed.
A hash of the user ID is used, so the HMAC part of the token is always
unique for each user.
It also hash a secret key, so without access to the source code,
fake tokens cannot be generated even if the database is compromised.
"""
timestamp = int(timestamp or time())
secret = to_bytes(secret)
key = '|'.join([
hashlib.sha1(secret).hexdigest(),
str(user.id),
get_hash_extract(user.password),
str(getattr(user, 'last_sign_in', 0)),
str(timestamp),
])
key = key.encode('utf8', 'ignore')
mac = hmac.new(key, msg=None, digestmod=hashlib.sha512)
mac = mac.hexdigest()[:50]
token = '{0}${1}${2}'.format(user.id, to36(timestamp), mac)
return token | [
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jpscaletti/authcode | authcode/utils.py | LazyUser.__get_user | def __get_user(self):
"""Return the real user object.
"""
storage = object.__getattribute__(self, '_LazyUser__storage')
user = getattr(self.__auth, 'get_user')()
setattr(storage, self.__user_name, user)
return user | python | def __get_user(self):
"""Return the real user object.
"""
storage = object.__getattribute__(self, '_LazyUser__storage')
user = getattr(self.__auth, 'get_user')()
setattr(storage, self.__user_name, user)
return user | [
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cloudmesh-cmd3/cmd3 | cmd3/plugins/browser.py | browser._expand_filename | def _expand_filename(self, line):
"""expands the filename if there is a . as leading path"""
# expand .
newline = line
path = os.getcwd()
if newline.startswith("."):
newline = newline.replace(".", path, 1)
# expand ~
newline = os.path.expanduser(newline)
return newline | python | def _expand_filename(self, line):
"""expands the filename if there is a . as leading path"""
# expand .
newline = line
path = os.getcwd()
if newline.startswith("."):
newline = newline.replace(".", path, 1)
# expand ~
newline = os.path.expanduser(newline)
return newline | [
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jstitch/MambuPy | MambuPy/rest/mambustruct.py | setCustomField | def setCustomField(mambuentity, customfield="", *args, **kwargs):
"""Modifies the customField field for the given object with
something related to the value of the given field.
If the dataType == "USER_LINK" then instead of using the value
of the CF, it will be a MambuUser object.
Same if dataType == "CLIENT_LINK", but with a MambuClient.
Default case: just uses the same value the CF already had.
Returns the number of requests done to Mambu.
"""
from . import mambuuser
from . import mambuclient
try:
customFieldValue = mambuentity[customfield]
# find the dataType customfield by name or id
datatype = [ l['customField']['dataType'] for l in mambuentity[mambuentity.customFieldName] if (l['name'] == customfield or l['id'] == customfield) ][0]
except IndexError as ierr:
# if no customfield found with the given name, assume it is a
# grouped custom field, name must have an index suffix that must
# be removed
try:
# find the dataType customfield by name or id
datatype = [ l['customField']['dataType'] for l in mambuentity[mambuentity.customFieldName] if (l['name'] == customfield.split('_')[0] or l['id'] == customfield.split('_')[0]) ][0]
except IndexError:
err = MambuError("Object %s has no custom field '%s'" % (mambuentity['id'], customfield))
raise err
except AttributeError:
err = MambuError("Object does not have a custom field to set")
raise err
if datatype == "USER_LINK":
mambuentity[customfield] = mambuuser.MambuUser(entid=customFieldValue, *args, **kwargs)
elif datatype == "CLIENT_LINK":
mambuentity[customfield] = mambuclient.MambuClient(entid=customFieldValue, *args, **kwargs)
else:
mambuentity[customfield] = customFieldValue
return 0
return 1 | python | def setCustomField(mambuentity, customfield="", *args, **kwargs):
"""Modifies the customField field for the given object with
something related to the value of the given field.
If the dataType == "USER_LINK" then instead of using the value
of the CF, it will be a MambuUser object.
Same if dataType == "CLIENT_LINK", but with a MambuClient.
Default case: just uses the same value the CF already had.
Returns the number of requests done to Mambu.
"""
from . import mambuuser
from . import mambuclient
try:
customFieldValue = mambuentity[customfield]
# find the dataType customfield by name or id
datatype = [ l['customField']['dataType'] for l in mambuentity[mambuentity.customFieldName] if (l['name'] == customfield or l['id'] == customfield) ][0]
except IndexError as ierr:
# if no customfield found with the given name, assume it is a
# grouped custom field, name must have an index suffix that must
# be removed
try:
# find the dataType customfield by name or id
datatype = [ l['customField']['dataType'] for l in mambuentity[mambuentity.customFieldName] if (l['name'] == customfield.split('_')[0] or l['id'] == customfield.split('_')[0]) ][0]
except IndexError:
err = MambuError("Object %s has no custom field '%s'" % (mambuentity['id'], customfield))
raise err
except AttributeError:
err = MambuError("Object does not have a custom field to set")
raise err
if datatype == "USER_LINK":
mambuentity[customfield] = mambuuser.MambuUser(entid=customFieldValue, *args, **kwargs)
elif datatype == "CLIENT_LINK":
mambuentity[customfield] = mambuclient.MambuClient(entid=customFieldValue, *args, **kwargs)
else:
mambuentity[customfield] = customFieldValue
return 0
return 1 | [
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jstitch/MambuPy | MambuPy/rest/mambustruct.py | MambuStruct.serializeFields | def serializeFields(data):
"""Turns every attribute of the Mambu object in to a string representation.
If the object is an iterable one, it goes down to each of its
elements and turns its attributes too, recursively.
The base case is when it's a MambuStruct class (this one) so it
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This is perhaps the worst way to do it, still looking for a better way.
"""
if isinstance(data, MambuStruct):
return data.serializeStruct()
try:
it = iter(data)
except TypeError as terr:
return unicode(data)
if type(it) == type(iter([])):
l = []
for e in it:
l.append(MambuStruct.serializeFields(e))
return l
elif type(it) == type(iter({})):
d = {}
for k in it:
d[k] = MambuStruct.serializeFields(data[k])
return d
# elif ... tuples? sets?
return unicode(data) | python | def serializeFields(data):
"""Turns every attribute of the Mambu object in to a string representation.
If the object is an iterable one, it goes down to each of its
elements and turns its attributes too, recursively.
The base case is when it's a MambuStruct class (this one) so it
just 'serializes' the attr atribute. Refer to
MambuStruct.serializeStruct pydoc.
This is perhaps the worst way to do it, still looking for a better way.
"""
if isinstance(data, MambuStruct):
return data.serializeStruct()
try:
it = iter(data)
except TypeError as terr:
return unicode(data)
if type(it) == type(iter([])):
l = []
for e in it:
l.append(MambuStruct.serializeFields(e))
return l
elif type(it) == type(iter({})):
d = {}
for k in it:
d[k] = MambuStruct.serializeFields(data[k])
return d
# elif ... tuples? sets?
return unicode(data) | [
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jstitch/MambuPy | MambuPy/rest/mambustruct.py | MambuStruct.init | def init(self, attrs={}, *args, **kwargs):
"""Default initialization from a dictionary responded by Mambu
in to the elements of the Mambu object.
It assings the response to attrs attribute and converts each of
its elements from a string to an adequate python object: number,
datetime, etc.
Basically it stores the response on the attrs attribute, then
runs some customizable preprocess method, then runs
convertDict2Attrs method to convert the string elements to an
adequate python object, then a customizable postprocess method.
It also executes each method on the 'methods' attribute given on
instantiation time, and sets new customizable 'properties' to
the object.
Why not on __init__? two reasons:
* __init__ optionally connects to Mambu, if you don't connect to
Mambu, the Mambu object will be configured but it won't have
any Mambu info on it. Only when connected, the Mambu object
will be initialized, here.
Useful to POST several times the same Mambu object. You make a
POST request over and over again by calling it's connect()
method every time you wish. This init method will configure the
response in to the attrs attribute each time.
You may also wish to update the info on a previously initialized
Mambu object and refresh it with what Mambu now has. Instead of
building a new object, you just connect() again and it will be
refreshed.
* Iterable Mambu objects (lists) do not initialize here, the
iterable Mambu object __init__ goes through each of its elements
and then initializes with this code one by one. Please look at
some Mambu iterable object code and pydoc for more details.
"""
self.attrs = attrs
self.preprocess()
self.convertDict2Attrs(*args, **kwargs)
self.postprocess()
try:
for meth in kwargs['methods']:
try:
getattr(self,meth)()
except Exception:
pass
except Exception:
pass
try:
for propname,propval in kwargs['properties'].items():
setattr(self,propname,propval)
except Exception:
pass | python | def init(self, attrs={}, *args, **kwargs):
"""Default initialization from a dictionary responded by Mambu
in to the elements of the Mambu object.
It assings the response to attrs attribute and converts each of
its elements from a string to an adequate python object: number,
datetime, etc.
Basically it stores the response on the attrs attribute, then
runs some customizable preprocess method, then runs
convertDict2Attrs method to convert the string elements to an
adequate python object, then a customizable postprocess method.
It also executes each method on the 'methods' attribute given on
instantiation time, and sets new customizable 'properties' to
the object.
Why not on __init__? two reasons:
* __init__ optionally connects to Mambu, if you don't connect to
Mambu, the Mambu object will be configured but it won't have
any Mambu info on it. Only when connected, the Mambu object
will be initialized, here.
Useful to POST several times the same Mambu object. You make a
POST request over and over again by calling it's connect()
method every time you wish. This init method will configure the
response in to the attrs attribute each time.
You may also wish to update the info on a previously initialized
Mambu object and refresh it with what Mambu now has. Instead of
building a new object, you just connect() again and it will be
refreshed.
* Iterable Mambu objects (lists) do not initialize here, the
iterable Mambu object __init__ goes through each of its elements
and then initializes with this code one by one. Please look at
some Mambu iterable object code and pydoc for more details.
"""
self.attrs = attrs
self.preprocess()
self.convertDict2Attrs(*args, **kwargs)
self.postprocess()
try:
for meth in kwargs['methods']:
try:
getattr(self,meth)()
except Exception:
pass
except Exception:
pass
try:
for propname,propval in kwargs['properties'].items():
setattr(self,propname,propval)
except Exception:
pass | [
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datetime, etc.
Basically it stores the response on the attrs attribute, then
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convertDict2Attrs method to convert the string elements to an
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It also executes each method on the 'methods' attribute given on
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* __init__ optionally connects to Mambu, if you don't connect to
Mambu, the Mambu object will be configured but it won't have
any Mambu info on it. Only when connected, the Mambu object
will be initialized, here.
Useful to POST several times the same Mambu object. You make a
POST request over and over again by calling it's connect()
method every time you wish. This init method will configure the
response in to the attrs attribute each time.
You may also wish to update the info on a previously initialized
Mambu object and refresh it with what Mambu now has. Instead of
building a new object, you just connect() again and it will be
refreshed.
* Iterable Mambu objects (lists) do not initialize here, the
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and then initializes with this code one by one. Please look at
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jstitch/MambuPy | MambuPy/rest/mambustruct.py | MambuStruct.connect | def connect(self, *args, **kwargs):
"""Connect to Mambu, make the request to the REST API.
If there's no urlfunc to use, nothing is done here.
When done, initializes the attrs attribute of the Mambu object
by calling the init method. Please refer to that code and pydoc
for further information.
Uses urllib module to connect. Since all Mambu REST API
responses are json, uses json module to translate the response
to a valid python object (dictionary or list).
When Mambu returns a response with returnCode and returnStatus
fields, it means something went wrong with the request, and a
MambuError is thrown detailing the error given by Mambu itself.
If you need to make a POST request, send a data argument to the
new Mambu object.
Provides to prevent errors due to using special chars on the
request URL. See mambuutil.iriToUri() method pydoc for further
info.
Provides to prevent errors due to using special chars on the
parameters of a POST request. See mambuutil.encoded_dict()
method pydoc for further info.
For every request done, the request counter Singleton is
increased.
Includes retry logic, to provide for a max number of connection
failures with Mambu. If maximum retries are reached,
MambuCommError is thrown.
Includes pagination code. Mambu supports a max of 500 elements
per response. Such an ugly detail is wrapped here so further
pagination logic is not needed above here. You need a million
elements? you got them by making several 500 elements requests
later joined together in a sigle list. Just send a limit=0
(default) and that's it.
.. todo:: improve raised exception messages. Sometimes
MambuCommErrors are thrown due to reasons not always
clear when catched down the road, but that perhaps may
be noticed in here and aren't fully reported to the
user. Specially serious on retries-MambuCommError
situations (the except Exception that increases the
retries counter is not saving the exception message,
just retrying).
.. todo:: what about using decorators for the retry and for the
window logic?
(https://www.oreilly.com/ideas/5-reasons-you-need-to-learn-to-write-python-decorators
# Reusing impossible-to-reuse code)
"""
from copy import deepcopy
if args:
self.__args = deepcopy(args)
if kwargs:
for k,v in kwargs.items():
self.__kwargs[k] = deepcopy(v)
jsresp = {}
if not self.__urlfunc:
return
# Pagination window, Mambu restricts at most 500 elements in response
offset = self.__offset
window = True
jsresp = {}
while window:
if not self.__limit or self.__limit > OUT_OF_BOUNDS_PAGINATION_LIMIT_VALUE:
limit = OUT_OF_BOUNDS_PAGINATION_LIMIT_VALUE
else:
limit = self.__limit
# Retry mechanism, for awful connections
retries = 0
while retries < MambuStruct.RETRIES:
try:
# Basic authentication
user = self.__kwargs.get('user', apiuser)
pwd = self.__kwargs.get('pwd', apipwd)
if self.__data:
headers = {'content-type': 'application/json'}
data = json.dumps(encoded_dict(self.__data))
url = iriToUri(self.__urlfunc(self.entid, limit=limit, offset=offset, *self.__args, **self.__kwargs))
# PATCH
if self.__method=="PATCH":
resp = requests.patch(url, data=data, headers=headers, auth=(user, pwd))
# POST
else:
resp = requests.post(url, data=data, headers=headers, auth=(user, pwd))
# GET
else:
url = iriToUri(self.__urlfunc(self.entid, limit=limit, offset=offset, *self.__args, **self.__kwargs))
resp = requests.get(url, auth=(user, pwd))
# Always count a new request when done!
self.rc.add(datetime.now())
try:
jsonresp = json.loads(resp.content)
# Returns list: extend list for offset
if type(jsonresp) == list:
try:
jsresp.extend(jsonresp)
except AttributeError:
# First window, forget that jsresp was a dict, turn it in to a list
jsresp=jsonresp
if len(jsonresp) < limit:
window = False
# Returns dict: in theory Mambu REST API doesn't takes limit/offset in to account
else:
jsresp = jsonresp
window = False
except ValueError as ex:
# json.loads invalid data argument
raise ex
except Exception as ex:
# any other json error
raise MambuError("JSON Error: %s" % repr(ex))
# if we reach here, we're done and safe
break
except MambuError as merr:
raise merr
except requests.exceptions.RequestException:
retries += 1
except Exception as ex:
raise ex
else:
raise MambuCommError("ERROR I can't communicate with Mambu")
# next window, moving offset...
offset = offset + limit
if self.__limit:
self.__limit -= limit
if self.__limit <= 0:
window = False
self.__limit = self.__inilimit
try:
if u'returnCode' in jsresp and u'returnStatus' in jsresp and jsresp[u'returnCode'] != 0:
raise MambuError(jsresp[u'returnStatus'])
except AttributeError:
pass
if self.__method != "PATCH":
self.init(attrs=jsresp, *self.__args, **self.__kwargs) | python | def connect(self, *args, **kwargs):
"""Connect to Mambu, make the request to the REST API.
If there's no urlfunc to use, nothing is done here.
When done, initializes the attrs attribute of the Mambu object
by calling the init method. Please refer to that code and pydoc
for further information.
Uses urllib module to connect. Since all Mambu REST API
responses are json, uses json module to translate the response
to a valid python object (dictionary or list).
When Mambu returns a response with returnCode and returnStatus
fields, it means something went wrong with the request, and a
MambuError is thrown detailing the error given by Mambu itself.
If you need to make a POST request, send a data argument to the
new Mambu object.
Provides to prevent errors due to using special chars on the
request URL. See mambuutil.iriToUri() method pydoc for further
info.
Provides to prevent errors due to using special chars on the
parameters of a POST request. See mambuutil.encoded_dict()
method pydoc for further info.
For every request done, the request counter Singleton is
increased.
Includes retry logic, to provide for a max number of connection
failures with Mambu. If maximum retries are reached,
MambuCommError is thrown.
Includes pagination code. Mambu supports a max of 500 elements
per response. Such an ugly detail is wrapped here so further
pagination logic is not needed above here. You need a million
elements? you got them by making several 500 elements requests
later joined together in a sigle list. Just send a limit=0
(default) and that's it.
.. todo:: improve raised exception messages. Sometimes
MambuCommErrors are thrown due to reasons not always
clear when catched down the road, but that perhaps may
be noticed in here and aren't fully reported to the
user. Specially serious on retries-MambuCommError
situations (the except Exception that increases the
retries counter is not saving the exception message,
just retrying).
.. todo:: what about using decorators for the retry and for the
window logic?
(https://www.oreilly.com/ideas/5-reasons-you-need-to-learn-to-write-python-decorators
# Reusing impossible-to-reuse code)
"""
from copy import deepcopy
if args:
self.__args = deepcopy(args)
if kwargs:
for k,v in kwargs.items():
self.__kwargs[k] = deepcopy(v)
jsresp = {}
if not self.__urlfunc:
return
# Pagination window, Mambu restricts at most 500 elements in response
offset = self.__offset
window = True
jsresp = {}
while window:
if not self.__limit or self.__limit > OUT_OF_BOUNDS_PAGINATION_LIMIT_VALUE:
limit = OUT_OF_BOUNDS_PAGINATION_LIMIT_VALUE
else:
limit = self.__limit
# Retry mechanism, for awful connections
retries = 0
while retries < MambuStruct.RETRIES:
try:
# Basic authentication
user = self.__kwargs.get('user', apiuser)
pwd = self.__kwargs.get('pwd', apipwd)
if self.__data:
headers = {'content-type': 'application/json'}
data = json.dumps(encoded_dict(self.__data))
url = iriToUri(self.__urlfunc(self.entid, limit=limit, offset=offset, *self.__args, **self.__kwargs))
# PATCH
if self.__method=="PATCH":
resp = requests.patch(url, data=data, headers=headers, auth=(user, pwd))
# POST
else:
resp = requests.post(url, data=data, headers=headers, auth=(user, pwd))
# GET
else:
url = iriToUri(self.__urlfunc(self.entid, limit=limit, offset=offset, *self.__args, **self.__kwargs))
resp = requests.get(url, auth=(user, pwd))
# Always count a new request when done!
self.rc.add(datetime.now())
try:
jsonresp = json.loads(resp.content)
# Returns list: extend list for offset
if type(jsonresp) == list:
try:
jsresp.extend(jsonresp)
except AttributeError:
# First window, forget that jsresp was a dict, turn it in to a list
jsresp=jsonresp
if len(jsonresp) < limit:
window = False
# Returns dict: in theory Mambu REST API doesn't takes limit/offset in to account
else:
jsresp = jsonresp
window = False
except ValueError as ex:
# json.loads invalid data argument
raise ex
except Exception as ex:
# any other json error
raise MambuError("JSON Error: %s" % repr(ex))
# if we reach here, we're done and safe
break
except MambuError as merr:
raise merr
except requests.exceptions.RequestException:
retries += 1
except Exception as ex:
raise ex
else:
raise MambuCommError("ERROR I can't communicate with Mambu")
# next window, moving offset...
offset = offset + limit
if self.__limit:
self.__limit -= limit
if self.__limit <= 0:
window = False
self.__limit = self.__inilimit
try:
if u'returnCode' in jsresp and u'returnStatus' in jsresp and jsresp[u'returnCode'] != 0:
raise MambuError(jsresp[u'returnStatus'])
except AttributeError:
pass
if self.__method != "PATCH":
self.init(attrs=jsresp, *self.__args, **self.__kwargs) | [
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If there's no urlfunc to use, nothing is done here.
When done, initializes the attrs attribute of the Mambu object
by calling the init method. Please refer to that code and pydoc
for further information.
Uses urllib module to connect. Since all Mambu REST API
responses are json, uses json module to translate the response
to a valid python object (dictionary or list).
When Mambu returns a response with returnCode and returnStatus
fields, it means something went wrong with the request, and a
MambuError is thrown detailing the error given by Mambu itself.
If you need to make a POST request, send a data argument to the
new Mambu object.
Provides to prevent errors due to using special chars on the
request URL. See mambuutil.iriToUri() method pydoc for further
info.
Provides to prevent errors due to using special chars on the
parameters of a POST request. See mambuutil.encoded_dict()
method pydoc for further info.
For every request done, the request counter Singleton is
increased.
Includes retry logic, to provide for a max number of connection
failures with Mambu. If maximum retries are reached,
MambuCommError is thrown.
Includes pagination code. Mambu supports a max of 500 elements
per response. Such an ugly detail is wrapped here so further
pagination logic is not needed above here. You need a million
elements? you got them by making several 500 elements requests
later joined together in a sigle list. Just send a limit=0
(default) and that's it.
.. todo:: improve raised exception messages. Sometimes
MambuCommErrors are thrown due to reasons not always
clear when catched down the road, but that perhaps may
be noticed in here and aren't fully reported to the
user. Specially serious on retries-MambuCommError
situations (the except Exception that increases the
retries counter is not saving the exception message,
just retrying).
.. todo:: what about using decorators for the retry and for the
window logic?
(https://www.oreilly.com/ideas/5-reasons-you-need-to-learn-to-write-python-decorators
# Reusing impossible-to-reuse code) | [
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] | 2af98cc12e7ed5ec183b3e97644e880e70b79ee8 | https://github.com/jstitch/MambuPy/blob/2af98cc12e7ed5ec183b3e97644e880e70b79ee8/MambuPy/rest/mambustruct.py#L516-L664 | train |
jstitch/MambuPy | MambuPy/rest/mambustruct.py | MambuStruct.convertDict2Attrs | def convertDict2Attrs(self, *args, **kwargs):
"""Each element on the atttrs attribute gest converted to a
proper python object, depending on type.
Some default constantFields are left as is (strings), because
they are better treated as strings.
"""
constantFields = ['id', 'groupName', 'name', 'homePhone', 'mobilePhone1', 'phoneNumber', 'postcode', 'emailAddress']
def convierte(data):
"""Recursively convert the fields on the data given to a python object."""
# Iterators, lists and dictionaries
# Here comes the recursive calls!
try:
it = iter(data)
if type(it) == type(iter({})):
d = {}
for k in it:
if k in constantFields:
d[k] = data[k]
else:
d[k] = convierte(data[k])
data = d
if type(it) == type(iter([])):
l = []
for e in it:
l.append(convierte(e))
data = l
except TypeError as terr:
pass
except Exception as ex:
raise ex
# Python built-in types: ints, floats, or even datetimes. If it
# cannot convert it to a built-in type, leave it as string, or
# as-is. There may be nested Mambu objects here!
# This are the recursion base cases!
try:
d = int(data)
if str(d) != data: # if string has trailing 0's, leave it as string, to not lose them
return data
return d
except (TypeError, ValueError) as tverr:
try:
return float(data)
except (TypeError, ValueError) as tverr:
try:
return self.util_dateFormat(data)
except (TypeError, ValueError) as tverr:
return data
return data
self.attrs = convierte(self.attrs) | python | def convertDict2Attrs(self, *args, **kwargs):
"""Each element on the atttrs attribute gest converted to a
proper python object, depending on type.
Some default constantFields are left as is (strings), because
they are better treated as strings.
"""
constantFields = ['id', 'groupName', 'name', 'homePhone', 'mobilePhone1', 'phoneNumber', 'postcode', 'emailAddress']
def convierte(data):
"""Recursively convert the fields on the data given to a python object."""
# Iterators, lists and dictionaries
# Here comes the recursive calls!
try:
it = iter(data)
if type(it) == type(iter({})):
d = {}
for k in it:
if k in constantFields:
d[k] = data[k]
else:
d[k] = convierte(data[k])
data = d
if type(it) == type(iter([])):
l = []
for e in it:
l.append(convierte(e))
data = l
except TypeError as terr:
pass
except Exception as ex:
raise ex
# Python built-in types: ints, floats, or even datetimes. If it
# cannot convert it to a built-in type, leave it as string, or
# as-is. There may be nested Mambu objects here!
# This are the recursion base cases!
try:
d = int(data)
if str(d) != data: # if string has trailing 0's, leave it as string, to not lose them
return data
return d
except (TypeError, ValueError) as tverr:
try:
return float(data)
except (TypeError, ValueError) as tverr:
try:
return self.util_dateFormat(data)
except (TypeError, ValueError) as tverr:
return data
return data
self.attrs = convierte(self.attrs) | [
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jstitch/MambuPy | MambuPy/rest/mambustruct.py | MambuStruct.util_dateFormat | def util_dateFormat(self, field, formato=None):
"""Converts a datetime field to a datetime using some specified format.
What this really means is that, if specified format includes
only for instance just year and month, day and further info gets
ignored and the objects get a datetime with year and month, and
day 1, hour 0, minute 0, etc.
A useful format may be %Y%m%d, then the datetime objects
effectively translates into date objects alone, with no relevant
time information.
PLEASE BE AWARE, that this may lose useful information for your
datetimes from Mambu. Read this for why this may be a BAD idea:
https://julien.danjou.info/blog/2015/python-and-timezones
"""
if not formato:
try:
formato = self.__formatoFecha
except AttributeError:
formato = "%Y-%m-%dT%H:%M:%S+0000"
return datetime.strptime(datetime.strptime(field, "%Y-%m-%dT%H:%M:%S+0000").strftime(formato), formato) | python | def util_dateFormat(self, field, formato=None):
"""Converts a datetime field to a datetime using some specified format.
What this really means is that, if specified format includes
only for instance just year and month, day and further info gets
ignored and the objects get a datetime with year and month, and
day 1, hour 0, minute 0, etc.
A useful format may be %Y%m%d, then the datetime objects
effectively translates into date objects alone, with no relevant
time information.
PLEASE BE AWARE, that this may lose useful information for your
datetimes from Mambu. Read this for why this may be a BAD idea:
https://julien.danjou.info/blog/2015/python-and-timezones
"""
if not formato:
try:
formato = self.__formatoFecha
except AttributeError:
formato = "%Y-%m-%dT%H:%M:%S+0000"
return datetime.strptime(datetime.strptime(field, "%Y-%m-%dT%H:%M:%S+0000").strftime(formato), formato) | [
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jstitch/MambuPy | MambuPy/rest/mambustruct.py | MambuStruct.create | def create(self, data, *args, **kwargs):
"""Creates an entity in Mambu
This method must be implemented in child classes
Args:
data (dictionary): dictionary with data to send, this dictionary
is specific for each Mambu entity
"""
# if module of the function is diferent from the module of the object
# that means create is not implemented in child class
if self.create.__func__.__module__ != self.__module__:
raise Exception("Child method not implemented")
self._MambuStruct__method = "POST"
self._MambuStruct__data = data
self.connect(*args, **kwargs)
self._MambuStruct__method = "GET"
self._MambuStruct__data = None | python | def create(self, data, *args, **kwargs):
"""Creates an entity in Mambu
This method must be implemented in child classes
Args:
data (dictionary): dictionary with data to send, this dictionary
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'''
Runs bcp FORMAT command to create a format file that will assist in creating the bulk data file
'''
with NamedTemporaryFile(delete=True) as f:
format_file = f.name + '.bcp-format'
format_args = cmd_args + ['format', NULL_FILE, '-c', '-f', format_file, '-t,'] + db_args
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self.load(format_file)
return format_file | python | def make(self, cmd_args, db_args):
'''
Runs bcp FORMAT command to create a format file that will assist in creating the bulk data file
'''
with NamedTemporaryFile(delete=True) as f:
format_file = f.name + '.bcp-format'
format_args = cmd_args + ['format', NULL_FILE, '-c', '-f', format_file, '-t,'] + db_args
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ExoticObjects/django-sql-server-bcp | django_sql_server_bcp/__init__.py | BCPFormat.load | def load(self, filename=None):
'''
Reads a non-XML bcp FORMAT file and parses it into fields list used for creating bulk data file
'''
fields = []
with open(filename, 'r') as f:
format_data = f.read().strip()
lines = format_data.split('\n')
self._sql_version = lines.pop(0)
self._num_fields = int(lines.pop(0))
for line in lines:
# Get rid of mulitple spaces
line = re.sub(' +', ' ', line.strip())
row_format = BCPFormatRow(line.split(' '))
fields.append(row_format)
self.fields = fields
self.filename = filename | python | def load(self, filename=None):
'''
Reads a non-XML bcp FORMAT file and parses it into fields list used for creating bulk data file
'''
fields = []
with open(filename, 'r') as f:
format_data = f.read().strip()
lines = format_data.split('\n')
self._sql_version = lines.pop(0)
self._num_fields = int(lines.pop(0))
for line in lines:
# Get rid of mulitple spaces
line = re.sub(' +', ' ', line.strip())
row_format = BCPFormatRow(line.split(' '))
fields.append(row_format)
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transifex/transifex-python-library | txlib/api/resources.py | Resource.retrieve_content | def retrieve_content(self):
"""Retrieve the content of a resource."""
path = self._construct_path_to_source_content()
res = self._http.get(path)
self._populated_fields['content'] = res['content']
return res['content'] | python | def retrieve_content(self):
"""Retrieve the content of a resource."""
path = self._construct_path_to_source_content()
res = self._http.get(path)
self._populated_fields['content'] = res['content']
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transifex/transifex-python-library | txlib/api/resources.py | Resource._update | def _update(self, **kwargs):
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path = self._construct_path_to_source_content()
self._http.put(path, json.dumps({'content': content}))
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"""Use separate URL for updating the source file."""
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content = kwargs.pop('content')
path = self._construct_path_to_source_content()
self._http.put(path, json.dumps({'content': content}))
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cloudmesh-cmd3/cmd3 | fabfile/clean.py | all | def all():
"""clean the dis and uninstall cloudmesh"""
dir()
cmd3()
banner("CLEAN PREVIOUS CLOUDMESH INSTALLS")
r = int(local("pip freeze |fgrep cloudmesh | wc -l", capture=True))
while r > 0:
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r = int(local("pip freeze |fgrep cloudmesh | wc -l", capture=True)) | python | def all():
"""clean the dis and uninstall cloudmesh"""
dir()
cmd3()
banner("CLEAN PREVIOUS CLOUDMESH INSTALLS")
r = int(local("pip freeze |fgrep cloudmesh | wc -l", capture=True))
while r > 0:
local('echo "y\n" | pip uninstall cloudmesh')
r = int(local("pip freeze |fgrep cloudmesh | wc -l", capture=True)) | [
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frostming/marko | marko/inline.py | InlineElement.find | def find(cls, text):
"""This method should return an iterable containing matches of this element."""
if isinstance(cls.pattern, string_types):
cls.pattern = re.compile(cls.pattern)
return cls.pattern.finditer(text) | python | def find(cls, text):
"""This method should return an iterable containing matches of this element."""
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youversion/crony | crony/crony.py | main | def main():
"""Entry point for running crony.
1. If a --cronitor/-c is specified, a "run" ping is sent to cronitor.
2. The argument string passed to crony is ran.
3. Next steps depend on the exit code of the command ran.
* If the exit status is 0 and a --cronitor/-c is specified, a "complete" ping is sent
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* If the exit status is greater than 0, a message is sent to Sentry with the output
captured from the script's exit.
* If the exit status is great than 0 and --cronitor/-c is specified, a "fail" ping
is sent to cronitor.
"""
parser = argparse.ArgumentParser(
description='Monitor your crons with cronitor.io & sentry.io',
epilog='https://github.com/youversion/crony',
prog='crony'
)
parser.add_argument('-c', '--cronitor', action='store',
help='Cronitor link identifier. This can be found in your Cronitor unique'
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parser.add_argument('-e', '--venv', action='store',
help='Path to virtualenv to source before running script. May be passed'
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parser.add_argument('-d', '--cd', action='store',
help='If the script needs ran in a specific directory, than can be passed'
' or cd can be ran prior to running crony.')
parser.add_argument('-l', '--log', action='store',
help='Log file to direct stdout of script run to. Can be passed or '
'defined in config file with "log_file"')
parser.add_argument('-o', '--config', action='store',
help='Path to a crony config file to use.')
parser.add_argument('-p', '--path', action='store',
help='Paths to append to the PATH environment variable before running. '
' Can be passed as an argument or loaded from config file.')
parser.add_argument('-s', '--dsn', action='store',
help='Sentry DSN. May be passed or loaded from an environment variable '
'or a config file.')
parser.add_argument('-t', '--timeout', action='store', default=10, help='Timeout to use when'
' sending requests to Cronitor', type=int)
parser.add_argument('-v', '--verbose', action='store_true', help='Increase level of verbosity'
' output by crony')
parser.add_argument('--version', action='store_true', help='Output crony version # and exit')
parser.add_argument('cmd', nargs=argparse.REMAINDER, help='Command to run and monitor')
cc = CommandCenter(parser.parse_args())
sys.exit(cc.log(*cc.func())) | python | def main():
"""Entry point for running crony.
1. If a --cronitor/-c is specified, a "run" ping is sent to cronitor.
2. The argument string passed to crony is ran.
3. Next steps depend on the exit code of the command ran.
* If the exit status is 0 and a --cronitor/-c is specified, a "complete" ping is sent
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* If the exit status is greater than 0, a message is sent to Sentry with the output
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* If the exit status is great than 0 and --cronitor/-c is specified, a "fail" ping
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"""
parser = argparse.ArgumentParser(
description='Monitor your crons with cronitor.io & sentry.io',
epilog='https://github.com/youversion/crony',
prog='crony'
)
parser.add_argument('-c', '--cronitor', action='store',
help='Cronitor link identifier. This can be found in your Cronitor unique'
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parser.add_argument('-e', '--venv', action='store',
help='Path to virtualenv to source before running script. May be passed'
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parser.add_argument('-d', '--cd', action='store',
help='If the script needs ran in a specific directory, than can be passed'
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parser.add_argument('-l', '--log', action='store',
help='Log file to direct stdout of script run to. Can be passed or '
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parser.add_argument('-o', '--config', action='store',
help='Path to a crony config file to use.')
parser.add_argument('-p', '--path', action='store',
help='Paths to append to the PATH environment variable before running. '
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parser.add_argument('-s', '--dsn', action='store',
help='Sentry DSN. May be passed or loaded from an environment variable '
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parser.add_argument('-t', '--timeout', action='store', default=10, help='Timeout to use when'
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parser.add_argument('-v', '--verbose', action='store_true', help='Increase level of verbosity'
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parser.add_argument('--version', action='store_true', help='Output crony version # and exit')
parser.add_argument('cmd', nargs=argparse.REMAINDER, help='Command to run and monitor')
cc = CommandCenter(parser.parse_args())
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youversion/crony | crony/crony.py | CommandCenter.cronitor | def cronitor(self):
"""Wrap run with requests to cronitor."""
url = f'https://cronitor.link/{self.opts.cronitor}/{{}}'
try:
run_url = url.format('run')
self.logger.debug(f'Pinging {run_url}')
requests.get(run_url, timeout=self.opts.timeout)
except requests.exceptions.RequestException as e:
self.logger.exception(e)
# Cronitor may be having an outage, but we still want to run our stuff
output, exit_status = self.run()
endpoint = 'complete' if exit_status == 0 else 'fail'
try:
ping_url = url.format(endpoint)
self.logger.debug('Pinging {}'.format(ping_url))
requests.get(ping_url, timeout=self.opts.timeout)
except requests.exceptions.RequestException as e:
self.logger.exception(e)
return output, exit_status | python | def cronitor(self):
"""Wrap run with requests to cronitor."""
url = f'https://cronitor.link/{self.opts.cronitor}/{{}}'
try:
run_url = url.format('run')
self.logger.debug(f'Pinging {run_url}')
requests.get(run_url, timeout=self.opts.timeout)
except requests.exceptions.RequestException as e:
self.logger.exception(e)
# Cronitor may be having an outage, but we still want to run our stuff
output, exit_status = self.run()
endpoint = 'complete' if exit_status == 0 else 'fail'
try:
ping_url = url.format(endpoint)
self.logger.debug('Pinging {}'.format(ping_url))
requests.get(ping_url, timeout=self.opts.timeout)
except requests.exceptions.RequestException as e:
self.logger.exception(e)
return output, exit_status | [
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youversion/crony | crony/crony.py | CommandCenter.load_config | def load_config(self, custom_config):
"""Attempt to load config from file.
If the command specified a --config parameter, then load that config file.
Otherwise, the user's home directory takes precedence over a system wide config.
Config file in the user's dir should be named ".cronyrc".
System wide config should be located at "/etc/crony.conf"
"""
self.config = configparser.ConfigParser()
if custom_config:
self.config.read(custom_config)
return f'Loading config from file {custom_config}.'
home = os.path.expanduser('~{}'.format(getpass.getuser()))
home_conf_file = os.path.join(home, '.cronyrc')
system_conf_file = '/etc/crony.conf'
conf_precedence = (home_conf_file, system_conf_file)
for conf_file in conf_precedence:
if os.path.exists(conf_file):
self.config.read(conf_file)
return f'Loading config from file {conf_file}.'
self.config['crony'] = {}
return 'No config file found.' | python | def load_config(self, custom_config):
"""Attempt to load config from file.
If the command specified a --config parameter, then load that config file.
Otherwise, the user's home directory takes precedence over a system wide config.
Config file in the user's dir should be named ".cronyrc".
System wide config should be located at "/etc/crony.conf"
"""
self.config = configparser.ConfigParser()
if custom_config:
self.config.read(custom_config)
return f'Loading config from file {custom_config}.'
home = os.path.expanduser('~{}'.format(getpass.getuser()))
home_conf_file = os.path.join(home, '.cronyrc')
system_conf_file = '/etc/crony.conf'
conf_precedence = (home_conf_file, system_conf_file)
for conf_file in conf_precedence:
if os.path.exists(conf_file):
self.config.read(conf_file)
return f'Loading config from file {conf_file}.'
self.config['crony'] = {}
return 'No config file found.' | [
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youversion/crony | crony/crony.py | CommandCenter.log | def log(self, output, exit_status):
"""Log given CompletedProcess and return exit status code."""
if exit_status != 0:
self.logger.error(f'Error running command! Exit status: {exit_status}, {output}')
return exit_status | python | def log(self, output, exit_status):
"""Log given CompletedProcess and return exit status code."""
if exit_status != 0:
self.logger.error(f'Error running command! Exit status: {exit_status}, {output}')
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youversion/crony | crony/crony.py | CommandCenter.run | def run(self):
"""Run command and report errors to Sentry."""
self.logger.debug(f'Running command: {self.cmd}')
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output = ""
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for stdout_line in iter(popen.stdout.readline, ""):
stdout_line = stdout_line.strip('\n')
output += stdout_line
yield stdout_line
popen.stdout.close()
return_code = popen.wait()
if return_code:
raise subprocess.CalledProcessError(return_code, cmd, output)
try:
for out in execute(self.cmd):
self.logger.info(out)
return "", 0
except subprocess.CalledProcessError as e:
return e.output, e.returncode | python | def run(self):
"""Run command and report errors to Sentry."""
self.logger.debug(f'Running command: {self.cmd}')
def execute(cmd):
output = ""
popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
universal_newlines=True, shell=True)
for stdout_line in iter(popen.stdout.readline, ""):
stdout_line = stdout_line.strip('\n')
output += stdout_line
yield stdout_line
popen.stdout.close()
return_code = popen.wait()
if return_code:
raise subprocess.CalledProcessError(return_code, cmd, output)
try:
for out in execute(self.cmd):
self.logger.info(out)
return "", 0
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youversion/crony | crony/crony.py | CommandCenter.setup_dir | def setup_dir(self):
"""Change directory for script if necessary."""
cd = self.opts.cd or self.config['crony'].get('directory')
if cd:
self.logger.debug(f'Adding cd to {cd}')
self.cmd = f'cd {cd} && {self.cmd}' | python | def setup_dir(self):
"""Change directory for script if necessary."""
cd = self.opts.cd or self.config['crony'].get('directory')
if cd:
self.logger.debug(f'Adding cd to {cd}')
self.cmd = f'cd {cd} && {self.cmd}' | [
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youversion/crony | crony/crony.py | CommandCenter.setup_logging | def setup_logging(self):
"""Setup python logging handler."""
date_format = '%Y-%m-%dT%H:%M:%S'
log_format = '%(asctime)s %(levelname)s: %(message)s'
if self.opts.verbose:
lvl = logging.DEBUG
else:
lvl = logging.INFO
# Requests is a bit chatty
logging.getLogger('requests').setLevel('WARNING')
self.logger.setLevel(lvl)
stdout = logging.StreamHandler(sys.stdout)
stdout.setLevel(lvl)
formatter = logging.Formatter(log_format, date_format)
stdout.setFormatter(formatter)
self.logger.addHandler(stdout)
# Decided not to use stderr
# stderr = logging.StreamHandler(sys.stderr)
# stderr.setLevel(logging.ERROR) # Error and above go to both stdout & stderr
# formatter = logging.Formatter(log_format, date_format)
# stderr.setFormatter(formatter)
# self.logger.addHandler(stderr)
log = self.opts.log or self.config['crony'].get('log_file')
if log:
logfile = logging.FileHandler(log)
logfile.setLevel(lvl)
formatter = logging.Formatter(log_format, date_format)
logfile.setFormatter(formatter)
self.logger.addHandler(logfile)
if self.sentry_client:
sentry = SentryHandler(self.sentry_client)
sentry.setLevel(logging.ERROR)
self.logger.addHandler(sentry)
self.logger.debug('Logging setup complete.') | python | def setup_logging(self):
"""Setup python logging handler."""
date_format = '%Y-%m-%dT%H:%M:%S'
log_format = '%(asctime)s %(levelname)s: %(message)s'
if self.opts.verbose:
lvl = logging.DEBUG
else:
lvl = logging.INFO
# Requests is a bit chatty
logging.getLogger('requests').setLevel('WARNING')
self.logger.setLevel(lvl)
stdout = logging.StreamHandler(sys.stdout)
stdout.setLevel(lvl)
formatter = logging.Formatter(log_format, date_format)
stdout.setFormatter(formatter)
self.logger.addHandler(stdout)
# Decided not to use stderr
# stderr = logging.StreamHandler(sys.stderr)
# stderr.setLevel(logging.ERROR) # Error and above go to both stdout & stderr
# formatter = logging.Formatter(log_format, date_format)
# stderr.setFormatter(formatter)
# self.logger.addHandler(stderr)
log = self.opts.log or self.config['crony'].get('log_file')
if log:
logfile = logging.FileHandler(log)
logfile.setLevel(lvl)
formatter = logging.Formatter(log_format, date_format)
logfile.setFormatter(formatter)
self.logger.addHandler(logfile)
if self.sentry_client:
sentry = SentryHandler(self.sentry_client)
sentry.setLevel(logging.ERROR)
self.logger.addHandler(sentry)
self.logger.debug('Logging setup complete.') | [
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youversion/crony | crony/crony.py | CommandCenter.setup_path | def setup_path(self):
"""Setup PATH env var if necessary."""
path = self.opts.path or self.config['crony'].get('path')
if path:
self.logger.debug(f'Adding {path} to PATH environment variable')
self.cmd = f'export PATH={path}:$PATH && {self.cmd}' | python | def setup_path(self):
"""Setup PATH env var if necessary."""
path = self.opts.path or self.config['crony'].get('path')
if path:
self.logger.debug(f'Adding {path} to PATH environment variable')
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youversion/crony | crony/crony.py | CommandCenter.setup_venv | def setup_venv(self):
"""Setup virtualenv if necessary."""
venv = self.opts.venv
if not venv:
venv = os.environ.get('CRONY_VENV')
if not venv and self.config['crony']:
venv = self.config['crony'].get('venv')
if venv:
if not venv.endswith('activate'):
add_path = os.path.join('bin', 'activate')
self.logger.debug(f'Venv directory given, adding {add_path}')
venv = os.path.join(venv, add_path)
self.logger.debug(f'Adding sourcing virtualenv {venv}')
self.cmd = f'. {venv} && {self.cmd}' | python | def setup_venv(self):
"""Setup virtualenv if necessary."""
venv = self.opts.venv
if not venv:
venv = os.environ.get('CRONY_VENV')
if not venv and self.config['crony']:
venv = self.config['crony'].get('venv')
if venv:
if not venv.endswith('activate'):
add_path = os.path.join('bin', 'activate')
self.logger.debug(f'Venv directory given, adding {add_path}')
venv = os.path.join(venv, add_path)
self.logger.debug(f'Adding sourcing virtualenv {venv}')
self.cmd = f'. {venv} && {self.cmd}' | [
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rsgalloway/grit | grit/repo/local.py | get_repos | def get_repos(path):
"""
Returns list of found branches.
:return: List of grit.Local objects
"""
p = str(path)
ret = []
if not os.path.exists(p):
return ret
for d in os.listdir(p):
pd = os.path.join(p, d)
if os.path.exists(pd) and is_repo(pd):
ret.append(Local(pd))
return ret | python | def get_repos(path):
"""
Returns list of found branches.
:return: List of grit.Local objects
"""
p = str(path)
ret = []
if not os.path.exists(p):
return ret
for d in os.listdir(p):
pd = os.path.join(p, d)
if os.path.exists(pd) and is_repo(pd):
ret.append(Local(pd))
return ret | [
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rsgalloway/grit | grit/repo/local.py | get_repo_parent | def get_repo_parent(path):
"""
Returns parent repo or input path if none found.
:return: grit.Local or path
"""
# path is a repository
if is_repo(path):
return Local(path)
# path is inside a repository
elif not os.path.isdir(path):
_rel = ''
while path and path != '/':
if is_repo(path):
return Local(path)
else:
_rel = os.path.join(os.path.basename(path), _rel)
path = os.path.dirname(path)
return path | python | def get_repo_parent(path):
"""
Returns parent repo or input path if none found.
:return: grit.Local or path
"""
# path is a repository
if is_repo(path):
return Local(path)
# path is inside a repository
elif not os.path.isdir(path):
_rel = ''
while path and path != '/':
if is_repo(path):
return Local(path)
else:
_rel = os.path.join(os.path.basename(path), _rel)
path = os.path.dirname(path)
return path | [
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rsgalloway/grit | grit/repo/local.py | Local.setVersion | def setVersion(self, version):
"""
Checkout a version of the repo.
:param version: Version number.
"""
try:
sha = self.versions(version).commit.sha
self.git.reset("--hard", sha)
except Exception, e:
raise RepoError(e) | python | def setVersion(self, version):
"""
Checkout a version of the repo.
:param version: Version number.
"""
try:
sha = self.versions(version).commit.sha
self.git.reset("--hard", sha)
except Exception, e:
raise RepoError(e) | [
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rsgalloway/grit | grit/repo/local.py | Local._commits | def _commits(self, head='HEAD'):
"""Returns a list of the commits reachable from head.
:return: List of commit objects. the first of which will be the commit
of head, then following theat will be the parents.
:raise: RepoError if any no commits are referenced, including if the
head parameter isn't the sha of a commit.
"""
pending_commits = [head]
history = []
while pending_commits != []:
head = pending_commits.pop(0)
try:
commit = self[head]
except KeyError:
raise KeyError(head)
if type(commit) != Commit:
raise TypeError(commit)
if commit in history:
continue
i = 0
for known_commit in history:
if known_commit.commit_time > commit.commit_time:
break
i += 1
history.insert(i, commit)
pending_commits += commit.parents
return history | python | def _commits(self, head='HEAD'):
"""Returns a list of the commits reachable from head.
:return: List of commit objects. the first of which will be the commit
of head, then following theat will be the parents.
:raise: RepoError if any no commits are referenced, including if the
head parameter isn't the sha of a commit.
"""
pending_commits = [head]
history = []
while pending_commits != []:
head = pending_commits.pop(0)
try:
commit = self[head]
except KeyError:
raise KeyError(head)
if type(commit) != Commit:
raise TypeError(commit)
if commit in history:
continue
i = 0
for known_commit in history:
if known_commit.commit_time > commit.commit_time:
break
i += 1
history.insert(i, commit)
pending_commits += commit.parents
return history | [
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rsgalloway/grit | grit/repo/local.py | Local.versions | def versions(self, version=None):
"""
List of Versions of this repository.
:param version: Version index.
:param rev: Commit sha or ref.
:return: List of Version objects matching params.
"""
try:
versions = [Version(self, c) for c in self._commits()]
except Exception, e:
log.debug('No versions exist')
return []
if version is not None and versions:
try:
versions = versions[version]
except IndexError:
raise VersionError('Version %s does not exist' % version)
return versions | python | def versions(self, version=None):
"""
List of Versions of this repository.
:param version: Version index.
:param rev: Commit sha or ref.
:return: List of Version objects matching params.
"""
try:
versions = [Version(self, c) for c in self._commits()]
except Exception, e:
log.debug('No versions exist')
return []
if version is not None and versions:
try:
versions = versions[version]
except IndexError:
raise VersionError('Version %s does not exist' % version)
return versions | [
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rsgalloway/grit | grit/repo/local.py | Local.setDescription | def setDescription(self, desc='No description'):
"""sets repository description"""
try:
self._put_named_file('description', desc)
except Exception, e:
raise RepoError(e) | python | def setDescription(self, desc='No description'):
"""sets repository description"""
try:
self._put_named_file('description', desc)
except Exception, e:
raise RepoError(e) | [
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rsgalloway/grit | grit/repo/local.py | Local.new | def new(self, path, desc=None, bare=True):
"""
Create a new bare repo.Local instance.
:param path: Path to new repo.
:param desc: Repo description.
:param bare: Create as bare repo.
:returns: New repo.Local instance.
"""
if os.path.exists(path):
raise RepoError('Path already exists: %s' % path)
try:
os.mkdir(path)
if bare:
Repo.init_bare(path)
else:
Repo.init(path)
repo = Local(path)
if desc:
repo.setDescription(desc)
version = repo.addVersion()
version.save('Repo Initialization')
return repo
except Exception, e:
traceback.print_exc()
raise RepoError('Error creating repo') | python | def new(self, path, desc=None, bare=True):
"""
Create a new bare repo.Local instance.
:param path: Path to new repo.
:param desc: Repo description.
:param bare: Create as bare repo.
:returns: New repo.Local instance.
"""
if os.path.exists(path):
raise RepoError('Path already exists: %s' % path)
try:
os.mkdir(path)
if bare:
Repo.init_bare(path)
else:
Repo.init(path)
repo = Local(path)
if desc:
repo.setDescription(desc)
version = repo.addVersion()
version.save('Repo Initialization')
return repo
except Exception, e:
traceback.print_exc()
raise RepoError('Error creating repo') | [
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rsgalloway/grit | grit/repo/local.py | Local.branch | def branch(self, name, desc=None):
"""
Create a branch of this repo at 'name'.
:param name: Name of new branch
:param desc: Repo description.
:return: New Local instance.
"""
return Local.new(path=os.path.join(self.path, name), desc=desc, bare=True) | python | def branch(self, name, desc=None):
"""
Create a branch of this repo at 'name'.
:param name: Name of new branch
:param desc: Repo description.
:return: New Local instance.
"""
return Local.new(path=os.path.join(self.path, name), desc=desc, bare=True) | [
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rsgalloway/grit | grit/repo/local.py | Local.addItem | def addItem(self, item, message=None):
"""add a new Item class object"""
if message is None:
message = 'Adding item %s' % item.path
try:
v = Version.new(repo=self)
v.addItem(item)
v.save(message)
except VersionError, e:
raise RepoError(e) | python | def addItem(self, item, message=None):
"""add a new Item class object"""
if message is None:
message = 'Adding item %s' % item.path
try:
v = Version.new(repo=self)
v.addItem(item)
v.save(message)
except VersionError, e:
raise RepoError(e) | [
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rsgalloway/grit | grit/repo/local.py | Local.items | def items(self, path=None, version=None):
"""
Returns a list of items.
:param path: Regex filter on item path.
:param version: Repo versions number/index.
:return: List of Item class objects.
"""
if version is None:
version = -1
items = {}
for item in self.versions(version).items():
items[item.path] = item
parent = self.parent
# get latest committed items from parents
while parent:
for item in parent.items(path=path):
if item.path not in items.keys():
items[item.path] = item
parent = parent.parent
# filter items matching path regex
if path is not None:
path += '$'
regex = re.compile(path)
return [item for path, item in items.items() if regex.match(path)]
else:
return items.values() | python | def items(self, path=None, version=None):
"""
Returns a list of items.
:param path: Regex filter on item path.
:param version: Repo versions number/index.
:return: List of Item class objects.
"""
if version is None:
version = -1
items = {}
for item in self.versions(version).items():
items[item.path] = item
parent = self.parent
# get latest committed items from parents
while parent:
for item in parent.items(path=path):
if item.path not in items.keys():
items[item.path] = item
parent = parent.parent
# filter items matching path regex
if path is not None:
path += '$'
regex = re.compile(path)
return [item for path, item in items.items() if regex.match(path)]
else:
return items.values() | [
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BernardFW/bernard | src/bernard/platforms/telegram/_utils.py | set_reply_markup | async def set_reply_markup(msg: Dict, request: 'Request', stack: 'Stack') \
-> None:
"""
Add the "reply markup" to a message from the layers
:param msg: Message dictionary
:param request: Current request being replied
:param stack: Stack to analyze
"""
from bernard.platforms.telegram.layers import InlineKeyboard, \
ReplyKeyboard, \
ReplyKeyboardRemove
try:
keyboard = stack.get_layer(InlineKeyboard)
except KeyError:
pass
else:
msg['reply_markup'] = await keyboard.serialize(request)
try:
keyboard = stack.get_layer(ReplyKeyboard)
except KeyError:
pass
else:
msg['reply_markup'] = await keyboard.serialize(request)
try:
remove = stack.get_layer(ReplyKeyboardRemove)
except KeyError:
pass
else:
msg['reply_markup'] = remove.serialize() | python | async def set_reply_markup(msg: Dict, request: 'Request', stack: 'Stack') \
-> None:
"""
Add the "reply markup" to a message from the layers
:param msg: Message dictionary
:param request: Current request being replied
:param stack: Stack to analyze
"""
from bernard.platforms.telegram.layers import InlineKeyboard, \
ReplyKeyboard, \
ReplyKeyboardRemove
try:
keyboard = stack.get_layer(InlineKeyboard)
except KeyError:
pass
else:
msg['reply_markup'] = await keyboard.serialize(request)
try:
keyboard = stack.get_layer(ReplyKeyboard)
except KeyError:
pass
else:
msg['reply_markup'] = await keyboard.serialize(request)
try:
remove = stack.get_layer(ReplyKeyboardRemove)
except KeyError:
pass
else:
msg['reply_markup'] = remove.serialize() | [
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BernardFW/bernard | src/bernard/i18n/utils.py | split_locale | def split_locale(locale: Text) -> Tuple[Text, Optional[Text]]:
"""
Decompose the locale into a normalized tuple.
The first item is the locale (as lowercase letters) while the second item
is either the country as lower case either None if no country was supplied.
"""
items = re.split(r'[_\-]', locale.lower(), 1)
try:
return items[0], items[1]
except IndexError:
return items[0], None | python | def split_locale(locale: Text) -> Tuple[Text, Optional[Text]]:
"""
Decompose the locale into a normalized tuple.
The first item is the locale (as lowercase letters) while the second item
is either the country as lower case either None if no country was supplied.
"""
items = re.split(r'[_\-]', locale.lower(), 1)
try:
return items[0], items[1]
except IndexError:
return items[0], None | [
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BernardFW/bernard | src/bernard/i18n/utils.py | compare_locales | def compare_locales(a, b):
"""
Compares two locales to find the level of compatibility
:param a: First locale
:param b: Second locale
:return: 2 full match, 1 lang match, 0 no match
"""
if a is None or b is None:
if a == b:
return 2
else:
return 0
a = split_locale(a)
b = split_locale(b)
if a == b:
return 2
elif a[0] == b[0]:
return 1
else:
return 0 | python | def compare_locales(a, b):
"""
Compares two locales to find the level of compatibility
:param a: First locale
:param b: Second locale
:return: 2 full match, 1 lang match, 0 no match
"""
if a is None or b is None:
if a == b:
return 2
else:
return 0
a = split_locale(a)
b = split_locale(b)
if a == b:
return 2
elif a[0] == b[0]:
return 1
else:
return 0 | [
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BernardFW/bernard | src/bernard/i18n/utils.py | LocalesDict.list_locales | def list_locales(self) -> List[Optional[Text]]:
"""
Returns the list of available locales. The first locale is the default
locale to be used. If no locales are known, then `None` will be the
first item.
"""
locales = list(self.dict.keys())
if not locales:
locales.append(None)
return locales | python | def list_locales(self) -> List[Optional[Text]]:
"""
Returns the list of available locales. The first locale is the default
locale to be used. If no locales are known, then `None` will be the
first item.
"""
locales = list(self.dict.keys())
if not locales:
locales.append(None)
return locales | [
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BernardFW/bernard | src/bernard/i18n/utils.py | LocalesDict.choose_locale | def choose_locale(self, locale: Text) -> Text:
"""
Returns the best matching locale in what is available.
:param locale: Locale to match
:return: Locale to use
"""
if locale not in self._choice_cache:
locales = self.list_locales()
best_choice = locales[0]
best_level = 0
for candidate in locales:
cmp = compare_locales(locale, candidate)
if cmp > best_level:
best_choice = candidate
best_level = cmp
self._choice_cache[locale] = best_choice
return self._choice_cache[locale] | python | def choose_locale(self, locale: Text) -> Text:
"""
Returns the best matching locale in what is available.
:param locale: Locale to match
:return: Locale to use
"""
if locale not in self._choice_cache:
locales = self.list_locales()
best_choice = locales[0]
best_level = 0
for candidate in locales:
cmp = compare_locales(locale, candidate)
if cmp > best_level:
best_choice = candidate
best_level = cmp
self._choice_cache[locale] = best_choice
return self._choice_cache[locale] | [
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BernardFW/bernard | src/bernard/i18n/utils.py | LocalesFlatDict.update | def update(self, new_data: Dict[Text, Dict[Text, Text]]):
"""
Receive an update from a loader.
:param new_data: New translation data from the loader
"""
for locale, data in new_data.items():
if locale not in self.dict:
self.dict[locale] = {}
self.dict[locale].update(data) | python | def update(self, new_data: Dict[Text, Dict[Text, Text]]):
"""
Receive an update from a loader.
:param new_data: New translation data from the loader
"""
for locale, data in new_data.items():
if locale not in self.dict:
self.dict[locale] = {}
self.dict[locale].update(data) | [
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BernardFW/bernard | src/bernard/platforms/facebook/helpers.py | UrlButton._make_url | async def _make_url(self, url: Text, request: 'Request') -> Text:
"""
Signs the URL if needed
"""
if self.sign_webview:
return await request.sign_url(url)
return url | python | async def _make_url(self, url: Text, request: 'Request') -> Text:
"""
Signs the URL if needed
"""
if self.sign_webview:
return await request.sign_url(url)
return url | [
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BernardFW/bernard | src/bernard/platforms/facebook/helpers.py | Card.is_sharable | def is_sharable(self):
"""
Make sure that nothing inside blocks sharing.
"""
if self.buttons:
return (all(b.is_sharable() for b in self.buttons) and
self.default_action and
self.default_action.is_sharable()) | python | def is_sharable(self):
"""
Make sure that nothing inside blocks sharing.
"""
if self.buttons:
return (all(b.is_sharable() for b in self.buttons) and
self.default_action and
self.default_action.is_sharable()) | [
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ioos/cc-plugin-ncei | cc_plugin_ncei/ncei_grid.py | NCEIGridBase.check_bounds_variables | def check_bounds_variables(self, dataset):
'''
Checks the grid boundary variables.
:param netCDF4.Dataset dataset: An open netCDF dataset
'''
recommended_ctx = TestCtx(BaseCheck.MEDIUM, 'Recommended variables to describe grid boundaries')
bounds_map = {
'lat_bounds': {
'units': 'degrees_north',
'comment': 'latitude values at the north and south bounds of each pixel.'
},
'lon_bounds': {
'units': 'degrees_east',
'comment': 'longitude values at the west and east bounds of each pixel.'
},
'z_bounds': {
'comment': 'z bounds for each z value',
},
'time_bounds': {
'comment': 'time bounds for each time value'
}
}
bounds_variables = [v.bounds for v in dataset.get_variables_by_attributes(bounds=lambda x: x is not None)]
for variable in bounds_variables:
ncvar = dataset.variables.get(variable, {})
recommended_ctx.assert_true(ncvar != {}, 'a variable {} should exist as indicated by a bounds attribute'.format(variable))
if ncvar == {}:
continue
units = getattr(ncvar, 'units', '')
if variable in bounds_map and 'units' in bounds_map[variable]:
recommended_ctx.assert_true(
units == bounds_map[variable]['units'],
'variable {} should have units {}'.format(variable, bounds_map[variable]['units'])
)
else:
recommended_ctx.assert_true(
units != '',
'variable {} should have a units attribute that is not empty'.format(variable)
)
comment = getattr(ncvar, 'comment', '')
recommended_ctx.assert_true(
comment != '',
'variable {} should have a comment and not be empty'
)
return recommended_ctx.to_result() | python | def check_bounds_variables(self, dataset):
'''
Checks the grid boundary variables.
:param netCDF4.Dataset dataset: An open netCDF dataset
'''
recommended_ctx = TestCtx(BaseCheck.MEDIUM, 'Recommended variables to describe grid boundaries')
bounds_map = {
'lat_bounds': {
'units': 'degrees_north',
'comment': 'latitude values at the north and south bounds of each pixel.'
},
'lon_bounds': {
'units': 'degrees_east',
'comment': 'longitude values at the west and east bounds of each pixel.'
},
'z_bounds': {
'comment': 'z bounds for each z value',
},
'time_bounds': {
'comment': 'time bounds for each time value'
}
}
bounds_variables = [v.bounds for v in dataset.get_variables_by_attributes(bounds=lambda x: x is not None)]
for variable in bounds_variables:
ncvar = dataset.variables.get(variable, {})
recommended_ctx.assert_true(ncvar != {}, 'a variable {} should exist as indicated by a bounds attribute'.format(variable))
if ncvar == {}:
continue
units = getattr(ncvar, 'units', '')
if variable in bounds_map and 'units' in bounds_map[variable]:
recommended_ctx.assert_true(
units == bounds_map[variable]['units'],
'variable {} should have units {}'.format(variable, bounds_map[variable]['units'])
)
else:
recommended_ctx.assert_true(
units != '',
'variable {} should have a units attribute that is not empty'.format(variable)
)
comment = getattr(ncvar, 'comment', '')
recommended_ctx.assert_true(
comment != '',
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return recommended_ctx.to_result() | [
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walter426/Python_GoogleMapsApi | GoogleMapsApi/geocode.py | Geocoding.geocode | def geocode(self, string, bounds=None, region=None,
language=None, sensor=False):
'''Geocode an address.
Pls refer to the Google Maps Web API for the details of the parameters
'''
if isinstance(string, unicode):
string = string.encode('utf-8')
params = {
'address': self.format_string % string,
'sensor': str(sensor).lower()
}
if bounds:
params['bounds'] = bounds
if region:
params['region'] = region
if language:
params['language'] = language
if not self.premier:
url = self.get_url(params)
else:
url = self.get_signed_url(params)
return self.GetService_url(url) | python | def geocode(self, string, bounds=None, region=None,
language=None, sensor=False):
'''Geocode an address.
Pls refer to the Google Maps Web API for the details of the parameters
'''
if isinstance(string, unicode):
string = string.encode('utf-8')
params = {
'address': self.format_string % string,
'sensor': str(sensor).lower()
}
if bounds:
params['bounds'] = bounds
if region:
params['region'] = region
if language:
params['language'] = language
if not self.premier:
url = self.get_url(params)
else:
url = self.get_signed_url(params)
return self.GetService_url(url) | [
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walter426/Python_GoogleMapsApi | GoogleMapsApi/geocode.py | Geocoding.reverse | def reverse(self, point, language=None, sensor=False):
'''Reverse geocode a point.
Pls refer to the Google Maps Web API for the details of the parameters
'''
params = {
'latlng': point,
'sensor': str(sensor).lower()
}
if language:
params['language'] = language
if not self.premier:
url = self.get_url(params)
else:
url = self.get_signed_url(params)
return self.GetService_url(url) | python | def reverse(self, point, language=None, sensor=False):
'''Reverse geocode a point.
Pls refer to the Google Maps Web API for the details of the parameters
'''
params = {
'latlng': point,
'sensor': str(sensor).lower()
}
if language:
params['language'] = language
if not self.premier:
url = self.get_url(params)
else:
url = self.get_signed_url(params)
return self.GetService_url(url) | [
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walter426/Python_GoogleMapsApi | GoogleMapsApi/directions.py | Directions.GetDirections | def GetDirections(self, origin, destination, sensor = False, mode = None, waypoints = None, alternatives = None, avoid = None, language = None, units = None,
region = None, departure_time = None, arrival_time = None):
'''Get Directions Service
Pls refer to the Google Maps Web API for the details of the remained parameters
'''
params = {
'origin': origin,
'destination': destination,
'sensor': str(sensor).lower()
}
if mode:
params['mode'] = mode
if waypoints:
params['waypoints'] = waypoints
if alternatives:
params['alternatives'] = alternatives
if avoid:
params['avoid'] = avoid
if language:
params['language'] = language
if units:
params['units'] = units
if region:
params['region'] = region
if departure_time:
params['departure_time'] = departure_time
if arrival_time:
params['arrival_time'] = arrival_time
if not self.premier:
url = self.get_url(params)
else:
url = self.get_signed_url(params)
return self.GetService_url(url) | python | def GetDirections(self, origin, destination, sensor = False, mode = None, waypoints = None, alternatives = None, avoid = None, language = None, units = None,
region = None, departure_time = None, arrival_time = None):
'''Get Directions Service
Pls refer to the Google Maps Web API for the details of the remained parameters
'''
params = {
'origin': origin,
'destination': destination,
'sensor': str(sensor).lower()
}
if mode:
params['mode'] = mode
if waypoints:
params['waypoints'] = waypoints
if alternatives:
params['alternatives'] = alternatives
if avoid:
params['avoid'] = avoid
if language:
params['language'] = language
if units:
params['units'] = units
if region:
params['region'] = region
if departure_time:
params['departure_time'] = departure_time
if arrival_time:
params['arrival_time'] = arrival_time
if not self.premier:
url = self.get_url(params)
else:
url = self.get_signed_url(params)
return self.GetService_url(url) | [
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sthysel/knobs | src/knobs.py | ListKnob.get | def get(self):
"""
convert json env variable if set to list
"""
self._cast = type([])
source_value = os.getenv(self.env_name)
# set the environment if it is not set
if source_value is None:
os.environ[self.env_name] = json.dumps(self.default)
return self.default
try:
val = json.loads(source_value)
except JSONDecodeError as e:
click.secho(str(e), err=True, color='red')
sys.exit(1)
except ValueError as e:
click.secho(e.message, err=True, color='red')
sys.exit(1)
if self.validator:
val = self.validator(val)
return val | python | def get(self):
"""
convert json env variable if set to list
"""
self._cast = type([])
source_value = os.getenv(self.env_name)
# set the environment if it is not set
if source_value is None:
os.environ[self.env_name] = json.dumps(self.default)
return self.default
try:
val = json.loads(source_value)
except JSONDecodeError as e:
click.secho(str(e), err=True, color='red')
sys.exit(1)
except ValueError as e:
click.secho(e.message, err=True, color='red')
sys.exit(1)
if self.validator:
val = self.validator(val)
return val | [
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/parsers.py | parse_ppi_graph | def parse_ppi_graph(path: str, min_edge_weight: float = 0.0) -> Graph:
"""Build an undirected graph of gene interactions from edgelist file.
:param str path: The path to the edgelist file
:param float min_edge_weight: Cutoff to keep/remove the edges, default is 0, but could also be 0.63.
:return Graph: Protein-protein interaction graph
"""
logger.info("In parse_ppi_graph()")
graph = igraph.read(os.path.expanduser(path), format="ncol", directed=False, names=True)
graph.delete_edges(graph.es.select(weight_lt=min_edge_weight))
graph.delete_vertices(graph.vs.select(_degree=0))
logger.info(f"Loaded PPI network.\n"
f"Number of proteins: {len(graph.vs)}\n"
f"Number of interactions: {len(graph.es)}\n")
return graph | python | def parse_ppi_graph(path: str, min_edge_weight: float = 0.0) -> Graph:
"""Build an undirected graph of gene interactions from edgelist file.
:param str path: The path to the edgelist file
:param float min_edge_weight: Cutoff to keep/remove the edges, default is 0, but could also be 0.63.
:return Graph: Protein-protein interaction graph
"""
logger.info("In parse_ppi_graph()")
graph = igraph.read(os.path.expanduser(path), format="ncol", directed=False, names=True)
graph.delete_edges(graph.es.select(weight_lt=min_edge_weight))
graph.delete_vertices(graph.vs.select(_degree=0))
logger.info(f"Loaded PPI network.\n"
f"Number of proteins: {len(graph.vs)}\n"
f"Number of interactions: {len(graph.es)}\n")
return graph | [
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GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/parsers.py | parse_excel | def parse_excel(file_path: str,
entrez_id_header,
log_fold_change_header,
adjusted_p_value_header,
entrez_delimiter,
base_mean_header=None) -> List[Gene]:
"""Read an excel file on differential expression values as Gene objects.
:param str file_path: The path to the differential expression file to be parsed.
:param config.Params params: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects.
"""
logger.info("In parse_excel()")
df = pd.read_excel(file_path)
return handle_dataframe(
df,
entrez_id_name=entrez_id_header,
log2_fold_change_name=log_fold_change_header,
adjusted_p_value_name=adjusted_p_value_header,
entrez_delimiter=entrez_delimiter,
base_mean=base_mean_header,
) | python | def parse_excel(file_path: str,
entrez_id_header,
log_fold_change_header,
adjusted_p_value_header,
entrez_delimiter,
base_mean_header=None) -> List[Gene]:
"""Read an excel file on differential expression values as Gene objects.
:param str file_path: The path to the differential expression file to be parsed.
:param config.Params params: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects.
"""
logger.info("In parse_excel()")
df = pd.read_excel(file_path)
return handle_dataframe(
df,
entrez_id_name=entrez_id_header,
log2_fold_change_name=log_fold_change_header,
adjusted_p_value_name=adjusted_p_value_header,
entrez_delimiter=entrez_delimiter,
base_mean=base_mean_header,
) | [
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:param str file_path: The path to the differential expression file to be parsed.
:param config.Params params: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects. | [
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] | 4d7b6713485f2d0a0957e6457edc1b1b5a237460 | https://github.com/GuiltyTargets/ppi-network-annotation/blob/4d7b6713485f2d0a0957e6457edc1b1b5a237460/src/ppi_network_annotation/parsers.py#L36-L59 | train |
GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/parsers.py | parse_csv | def parse_csv(file_path: str,
entrez_id_header,
log_fold_change_header,
adjusted_p_value_header,
entrez_delimiter,
base_mean_header=None,
sep=",") -> List[Gene]:
"""Read a csv file on differential expression values as Gene objects.
:param str file_path: The path to the differential expression file to be parsed.
:param config.Params params: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects.
"""
logger.info("In parse_csv()")
df = pd.read_csv(file_path, sep=sep)
return handle_dataframe(
df,
entrez_id_name=entrez_id_header,
log2_fold_change_name=log_fold_change_header,
adjusted_p_value_name=adjusted_p_value_header,
entrez_delimiter=entrez_delimiter,
base_mean=base_mean_header,
) | python | def parse_csv(file_path: str,
entrez_id_header,
log_fold_change_header,
adjusted_p_value_header,
entrez_delimiter,
base_mean_header=None,
sep=",") -> List[Gene]:
"""Read a csv file on differential expression values as Gene objects.
:param str file_path: The path to the differential expression file to be parsed.
:param config.Params params: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects.
"""
logger.info("In parse_csv()")
df = pd.read_csv(file_path, sep=sep)
return handle_dataframe(
df,
entrez_id_name=entrez_id_header,
log2_fold_change_name=log_fold_change_header,
adjusted_p_value_name=adjusted_p_value_header,
entrez_delimiter=entrez_delimiter,
base_mean=base_mean_header,
) | [
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:param str file_path: The path to the differential expression file to be parsed.
:param config.Params params: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects. | [
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] | 4d7b6713485f2d0a0957e6457edc1b1b5a237460 | https://github.com/GuiltyTargets/ppi-network-annotation/blob/4d7b6713485f2d0a0957e6457edc1b1b5a237460/src/ppi_network_annotation/parsers.py#L62-L86 | train |
GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/parsers.py | handle_dataframe | def handle_dataframe(
df: pd.DataFrame,
entrez_id_name,
log2_fold_change_name,
adjusted_p_value_name,
entrez_delimiter,
base_mean=None,
) -> List[Gene]:
"""Convert data frame on differential expression values as Gene objects.
:param df: Data frame with columns showing values on differential
expression.
:param cfp: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects.
"""
logger.info("In _handle_df()")
if base_mean is not None and base_mean in df.columns:
df = df[pd.notnull(df[base_mean])]
df = df[pd.notnull(df[entrez_id_name])]
df = df[pd.notnull(df[log2_fold_change_name])]
df = df[pd.notnull(df[adjusted_p_value_name])]
# try:
# import bio2bel_hgnc
# except ImportError:
# logger.debug('skipping mapping')
# else:
# manager = bio2bel_hgnc.Manager()
# # TODO @cthoyt
return [
Gene(
entrez_id=entrez_id,
log2_fold_change=data[log2_fold_change_name],
padj=data[adjusted_p_value_name]
)
for _, data in df.iterrows()
for entrez_id in str(data[entrez_id_name]).split(entrez_delimiter)
] | python | def handle_dataframe(
df: pd.DataFrame,
entrez_id_name,
log2_fold_change_name,
adjusted_p_value_name,
entrez_delimiter,
base_mean=None,
) -> List[Gene]:
"""Convert data frame on differential expression values as Gene objects.
:param df: Data frame with columns showing values on differential
expression.
:param cfp: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects.
"""
logger.info("In _handle_df()")
if base_mean is not None and base_mean in df.columns:
df = df[pd.notnull(df[base_mean])]
df = df[pd.notnull(df[entrez_id_name])]
df = df[pd.notnull(df[log2_fold_change_name])]
df = df[pd.notnull(df[adjusted_p_value_name])]
# try:
# import bio2bel_hgnc
# except ImportError:
# logger.debug('skipping mapping')
# else:
# manager = bio2bel_hgnc.Manager()
# # TODO @cthoyt
return [
Gene(
entrez_id=entrez_id,
log2_fold_change=data[log2_fold_change_name],
padj=data[adjusted_p_value_name]
)
for _, data in df.iterrows()
for entrez_id in str(data[entrez_id_name]).split(entrez_delimiter)
] | [
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:param df: Data frame with columns showing values on differential
expression.
:param cfp: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects. | [
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] | 4d7b6713485f2d0a0957e6457edc1b1b5a237460 | https://github.com/GuiltyTargets/ppi-network-annotation/blob/4d7b6713485f2d0a0957e6457edc1b1b5a237460/src/ppi_network_annotation/parsers.py#L89-L129 | train |
GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/parsers.py | parse_gene_list | def parse_gene_list(path: str, graph: Graph, anno_type: str = "name") -> list:
"""Parse a list of genes and return them if they are in the network.
:param str path: The path of input file.
:param Graph graph: The graph with genes as nodes.
:param str anno_type: The type of annotation with two options:name-Entrez ID, symbol-HGNC symbol.
:return list: A list of genes, all of which are in the network.
"""
# read the file
genes = pd.read_csv(path, header=None)[0].tolist()
genes = [str(int(gene)) for gene in genes]
# get those genes which are in the network
ind = []
if anno_type == "name":
ind = graph.vs.select(name_in=genes).indices
elif anno_type == "symbol":
ind = graph.vs.select(symbol_in=genes).indices
else:
raise Exception("The type can either be name or symbol, {} is not "
"supported".format(anno_type))
genes = graph.vs[ind][anno_type]
return genes | python | def parse_gene_list(path: str, graph: Graph, anno_type: str = "name") -> list:
"""Parse a list of genes and return them if they are in the network.
:param str path: The path of input file.
:param Graph graph: The graph with genes as nodes.
:param str anno_type: The type of annotation with two options:name-Entrez ID, symbol-HGNC symbol.
:return list: A list of genes, all of which are in the network.
"""
# read the file
genes = pd.read_csv(path, header=None)[0].tolist()
genes = [str(int(gene)) for gene in genes]
# get those genes which are in the network
ind = []
if anno_type == "name":
ind = graph.vs.select(name_in=genes).indices
elif anno_type == "symbol":
ind = graph.vs.select(symbol_in=genes).indices
else:
raise Exception("The type can either be name or symbol, {} is not "
"supported".format(anno_type))
genes = graph.vs[ind][anno_type]
return genes | [
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:param str path: The path of input file.
:param Graph graph: The graph with genes as nodes.
:param str anno_type: The type of annotation with two options:name-Entrez ID, symbol-HGNC symbol.
:return list: A list of genes, all of which are in the network. | [
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] | 4d7b6713485f2d0a0957e6457edc1b1b5a237460 | https://github.com/GuiltyTargets/ppi-network-annotation/blob/4d7b6713485f2d0a0957e6457edc1b1b5a237460/src/ppi_network_annotation/parsers.py#L132-L155 | train |
GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/parsers.py | parse_disease_ids | def parse_disease_ids(path: str):
"""Parse the disease identifier file.
:param str path: Path to the disease identifier file.
:return: List of disease identifiers.
"""
if os.path.isdir(path) or not os.path.exists(path):
logger.info("Couldn't find the disease identifiers file. Returning empty list.")
return []
df = pd.read_csv(path, names=["ID"])
return set(df["ID"].tolist()) | python | def parse_disease_ids(path: str):
"""Parse the disease identifier file.
:param str path: Path to the disease identifier file.
:return: List of disease identifiers.
"""
if os.path.isdir(path) or not os.path.exists(path):
logger.info("Couldn't find the disease identifiers file. Returning empty list.")
return []
df = pd.read_csv(path, names=["ID"])
return set(df["ID"].tolist()) | [
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:param str path: Path to the disease identifier file.
:return: List of disease identifiers. | [
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] | 4d7b6713485f2d0a0957e6457edc1b1b5a237460 | https://github.com/GuiltyTargets/ppi-network-annotation/blob/4d7b6713485f2d0a0957e6457edc1b1b5a237460/src/ppi_network_annotation/parsers.py#L158-L169 | train |
GuiltyTargets/ppi-network-annotation | src/ppi_network_annotation/parsers.py | parse_disease_associations | def parse_disease_associations(path: str, excluded_disease_ids: set):
"""Parse the disease-drug target associations file.
:param str path: Path to the disease-drug target associations file.
:param list excluded_disease_ids: Identifiers of the disease for which drug targets are being predicted.
:return: Dictionary of drug target-disease mappings.
"""
if os.path.isdir(path) or not os.path.exists(path):
logger.info("Couldn't find the disease associations file. Returning empty list.")
return {}
disease_associations = defaultdict(list)
with open(path) as input_file:
for line in input_file:
target_id, disease_id = line.strip().split(" ")
if disease_id not in excluded_disease_ids:
disease_associations[target_id].append(disease_id)
return disease_associations | python | def parse_disease_associations(path: str, excluded_disease_ids: set):
"""Parse the disease-drug target associations file.
:param str path: Path to the disease-drug target associations file.
:param list excluded_disease_ids: Identifiers of the disease for which drug targets are being predicted.
:return: Dictionary of drug target-disease mappings.
"""
if os.path.isdir(path) or not os.path.exists(path):
logger.info("Couldn't find the disease associations file. Returning empty list.")
return {}
disease_associations = defaultdict(list)
with open(path) as input_file:
for line in input_file:
target_id, disease_id = line.strip().split(" ")
if disease_id not in excluded_disease_ids:
disease_associations[target_id].append(disease_id)
return disease_associations | [
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:param str path: Path to the disease-drug target associations file.
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:return: Dictionary of drug target-disease mappings. | [
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