repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
infobloxopen/infoblox-client | infoblox_client/object_manager.py | InfobloxObjectManager.create_ip_range | def create_ip_range(self, network_view, start_ip, end_ip, network,
disable, range_extattrs):
"""Creates IPRange or fails if already exists."""
return obj.IPRange.create(self.connector,
network_view=network_view,
... | python | def create_ip_range(self, network_view, start_ip, end_ip, network,
disable, range_extattrs):
"""Creates IPRange or fails if already exists."""
return obj.IPRange.create(self.connector,
network_view=network_view,
... | Creates IPRange or fails if already exists. | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/object_manager.py#L103-L113 |
infobloxopen/infoblox-client | infoblox_client/object_manager.py | InfobloxObjectManager.network_exists | def network_exists(self, network_view, cidr):
"""Deprecated, use get_network() instead."""
LOG.warning(
"DEPRECATION WARNING! Using network_exists() is deprecated "
"and to be removed in next releases. "
"Use get_network() or objects.Network.search instead")
n... | python | def network_exists(self, network_view, cidr):
"""Deprecated, use get_network() instead."""
LOG.warning(
"DEPRECATION WARNING! Using network_exists() is deprecated "
"and to be removed in next releases. "
"Use get_network() or objects.Network.search instead")
n... | Deprecated, use get_network() instead. | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/object_manager.py#L128-L137 |
infobloxopen/infoblox-client | infoblox_client/object_manager.py | InfobloxObjectManager.delete_objects_associated_with_a_record | def delete_objects_associated_with_a_record(self, name, view, delete_list):
"""Deletes records associated with record:a or record:aaaa."""
search_objects = {}
if 'record:cname' in delete_list:
search_objects['record:cname'] = 'canonical'
if 'record:txt' in delete_list:
... | python | def delete_objects_associated_with_a_record(self, name, view, delete_list):
"""Deletes records associated with record:a or record:aaaa."""
search_objects = {}
if 'record:cname' in delete_list:
search_objects['record:cname'] = 'canonical'
if 'record:txt' in delete_list:
... | Deletes records associated with record:a or record:aaaa. | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/object_manager.py#L453-L470 |
infobloxopen/infoblox-client | infoblox_client/connector.py | Connector._parse_options | def _parse_options(self, options):
"""Copy needed options to self"""
attributes = ('host', 'wapi_version', 'username', 'password',
'ssl_verify', 'http_request_timeout', 'max_retries',
'http_pool_connections', 'http_pool_maxsize',
'silent_... | python | def _parse_options(self, options):
"""Copy needed options to self"""
attributes = ('host', 'wapi_version', 'username', 'password',
'ssl_verify', 'http_request_timeout', 'max_retries',
'http_pool_connections', 'http_pool_maxsize',
'silent_... | Copy needed options to self | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/connector.py#L89-L115 |
infobloxopen/infoblox-client | infoblox_client/connector.py | Connector._parse_reply | def _parse_reply(request):
"""Tries to parse reply from NIOS.
Raises exception with content if reply is not in json format
"""
try:
return jsonutils.loads(request.content)
except ValueError:
raise ib_ex.InfobloxConnectionError(reason=request.content) | python | def _parse_reply(request):
"""Tries to parse reply from NIOS.
Raises exception with content if reply is not in json format
"""
try:
return jsonutils.loads(request.content)
except ValueError:
raise ib_ex.InfobloxConnectionError(reason=request.content) | Tries to parse reply from NIOS.
Raises exception with content if reply is not in json format | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/connector.py#L212-L220 |
infobloxopen/infoblox-client | infoblox_client/connector.py | Connector.get_object | def get_object(self, obj_type, payload=None, return_fields=None,
extattrs=None, force_proxy=False, max_results=None,
paging=False):
"""Retrieve a list of Infoblox objects of type 'obj_type'
Some get requests like 'ipv4address' should be always
proxied to GM... | python | def get_object(self, obj_type, payload=None, return_fields=None,
extattrs=None, force_proxy=False, max_results=None,
paging=False):
"""Retrieve a list of Infoblox objects of type 'obj_type'
Some get requests like 'ipv4address' should be always
proxied to GM... | Retrieve a list of Infoblox objects of type 'obj_type'
Some get requests like 'ipv4address' should be always
proxied to GM on Hellfire
If request is cloud and proxy is not forced yet,
then plan to do 2 request:
- the first one is not proxied to GM
- the second is proxied... | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/connector.py#L231-L293 |
infobloxopen/infoblox-client | infoblox_client/connector.py | Connector.create_object | def create_object(self, obj_type, payload, return_fields=None):
"""Create an Infoblox object of type 'obj_type'
Args:
obj_type (str): Infoblox object type,
e.g. 'network', 'range', etc.
payload (dict): Payload with data to send
... | python | def create_object(self, obj_type, payload, return_fields=None):
"""Create an Infoblox object of type 'obj_type'
Args:
obj_type (str): Infoblox object type,
e.g. 'network', 'range', etc.
payload (dict): Payload with data to send
... | Create an Infoblox object of type 'obj_type'
Args:
obj_type (str): Infoblox object type,
e.g. 'network', 'range', etc.
payload (dict): Payload with data to send
return_fields (list): List of fields to be returned
Returns... | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/connector.py#L345-L387 |
infobloxopen/infoblox-client | infoblox_client/connector.py | Connector.update_object | def update_object(self, ref, payload, return_fields=None):
"""Update an Infoblox object
Args:
ref (str): Infoblox object reference
payload (dict): Payload with data to send
Returns:
The object reference of the updated object
Raises:
I... | python | def update_object(self, ref, payload, return_fields=None):
"""Update an Infoblox object
Args:
ref (str): Infoblox object reference
payload (dict): Payload with data to send
Returns:
The object reference of the updated object
Raises:
I... | Update an Infoblox object
Args:
ref (str): Infoblox object reference
payload (dict): Payload with data to send
Returns:
The object reference of the updated object
Raises:
InfobloxException | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/connector.py#L424-L453 |
infobloxopen/infoblox-client | infoblox_client/connector.py | Connector.delete_object | def delete_object(self, ref, delete_arguments=None):
"""Remove an Infoblox object
Args:
ref (str): Object reference
delete_arguments (dict): Extra delete arguments
Returns:
The object reference of the removed object
Raises:
I... | python | def delete_object(self, ref, delete_arguments=None):
"""Remove an Infoblox object
Args:
ref (str): Object reference
delete_arguments (dict): Extra delete arguments
Returns:
The object reference of the removed object
Raises:
I... | Remove an Infoblox object
Args:
ref (str): Object reference
delete_arguments (dict): Extra delete arguments
Returns:
The object reference of the removed object
Raises:
InfobloxException | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/connector.py#L456-L485 |
infobloxopen/infoblox-client | infoblox_client/objects.py | BaseObject._remap_fields | def _remap_fields(cls, kwargs):
"""Map fields from kwargs into dict acceptable by NIOS"""
mapped = {}
for key in kwargs:
if key in cls._remap:
mapped[cls._remap[key]] = kwargs[key]
else:
mapped[key] = kwargs[key]
return mapped | python | def _remap_fields(cls, kwargs):
"""Map fields from kwargs into dict acceptable by NIOS"""
mapped = {}
for key in kwargs:
if key in cls._remap:
mapped[cls._remap[key]] = kwargs[key]
else:
mapped[key] = kwargs[key]
return mapped | Map fields from kwargs into dict acceptable by NIOS | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L87-L95 |
infobloxopen/infoblox-client | infoblox_client/objects.py | EA.from_dict | def from_dict(cls, eas_from_nios):
"""Converts extensible attributes from the NIOS reply."""
if not eas_from_nios:
return
return cls({name: cls._process_value(ib_utils.try_value_to_bool,
eas_from_nios[name]['value'])
fo... | python | def from_dict(cls, eas_from_nios):
"""Converts extensible attributes from the NIOS reply."""
if not eas_from_nios:
return
return cls({name: cls._process_value(ib_utils.try_value_to_bool,
eas_from_nios[name]['value'])
fo... | Converts extensible attributes from the NIOS reply. | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L141-L147 |
infobloxopen/infoblox-client | infoblox_client/objects.py | EA.to_dict | def to_dict(self):
"""Converts extensible attributes into the format suitable for NIOS."""
return {name: {'value': self._process_value(str, value)}
for name, value in self._ea_dict.items()
if not (value is None or value == "" or value == [])} | python | def to_dict(self):
"""Converts extensible attributes into the format suitable for NIOS."""
return {name: {'value': self._process_value(str, value)}
for name, value in self._ea_dict.items()
if not (value is None or value == "" or value == [])} | Converts extensible attributes into the format suitable for NIOS. | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L149-L153 |
infobloxopen/infoblox-client | infoblox_client/objects.py | EA._process_value | def _process_value(func, value):
"""Applies processing method for value or each element in it.
:param func: method to be called with value
:param value: value to process
:return: if 'value' is list/tupe, returns iterable with func results,
else func result is returned
... | python | def _process_value(func, value):
"""Applies processing method for value or each element in it.
:param func: method to be called with value
:param value: value to process
:return: if 'value' is list/tupe, returns iterable with func results,
else func result is returned
... | Applies processing method for value or each element in it.
:param func: method to be called with value
:param value: value to process
:return: if 'value' is list/tupe, returns iterable with func results,
else func result is returned | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L156-L166 |
infobloxopen/infoblox-client | infoblox_client/objects.py | InfobloxObject.from_dict | def from_dict(cls, connector, ip_dict):
"""Build dict fields as SubObjects if needed.
Checks if lambda for building object from dict exists.
_global_field_processing and _custom_field_processing rules
are checked.
"""
mapping = cls._global_field_processing.copy()
... | python | def from_dict(cls, connector, ip_dict):
"""Build dict fields as SubObjects if needed.
Checks if lambda for building object from dict exists.
_global_field_processing and _custom_field_processing rules
are checked.
"""
mapping = cls._global_field_processing.copy()
... | Build dict fields as SubObjects if needed.
Checks if lambda for building object from dict exists.
_global_field_processing and _custom_field_processing rules
are checked. | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L243-L256 |
infobloxopen/infoblox-client | infoblox_client/objects.py | InfobloxObject.field_to_dict | def field_to_dict(self, field):
"""Read field value and converts to dict if possible"""
value = getattr(self, field)
if isinstance(value, (list, tuple)):
return [self.value_to_dict(val) for val in value]
return self.value_to_dict(value) | python | def field_to_dict(self, field):
"""Read field value and converts to dict if possible"""
value = getattr(self, field)
if isinstance(value, (list, tuple)):
return [self.value_to_dict(val) for val in value]
return self.value_to_dict(value) | Read field value and converts to dict if possible | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L262-L267 |
infobloxopen/infoblox-client | infoblox_client/objects.py | InfobloxObject.to_dict | def to_dict(self, search_fields=None):
"""Builds dict without None object fields"""
fields = self._fields
if search_fields == 'update':
fields = self._search_for_update_fields
elif search_fields == 'all':
fields = self._all_searchable_fields
elif search_fi... | python | def to_dict(self, search_fields=None):
"""Builds dict without None object fields"""
fields = self._fields
if search_fields == 'update':
fields = self._search_for_update_fields
elif search_fields == 'all':
fields = self._all_searchable_fields
elif search_fi... | Builds dict without None object fields | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L269-L284 |
infobloxopen/infoblox-client | infoblox_client/objects.py | InfobloxObject.fetch | def fetch(self, only_ref=False):
"""Fetch object from NIOS by _ref or searchfields
Update existent object with fields returned from NIOS
Return True on successful object fetch
"""
if self.ref:
reply = self.connector.get_object(
self.ref, return_fields... | python | def fetch(self, only_ref=False):
"""Fetch object from NIOS by _ref or searchfields
Update existent object with fields returned from NIOS
Return True on successful object fetch
"""
if self.ref:
reply = self.connector.get_object(
self.ref, return_fields... | Fetch object from NIOS by _ref or searchfields
Update existent object with fields returned from NIOS
Return True on successful object fetch | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L378-L399 |
infobloxopen/infoblox-client | infoblox_client/objects.py | HostRecord._ip_setter | def _ip_setter(self, ipaddr_name, ipaddrs_name, ips):
"""Setter for ip fields
Accept as input string or list of IP instances.
String case:
only ipvXaddr is going to be filled, that is enough to perform
host record search using ip
List of IP instances case:
... | python | def _ip_setter(self, ipaddr_name, ipaddrs_name, ips):
"""Setter for ip fields
Accept as input string or list of IP instances.
String case:
only ipvXaddr is going to be filled, that is enough to perform
host record search using ip
List of IP instances case:
... | Setter for ip fields
Accept as input string or list of IP instances.
String case:
only ipvXaddr is going to be filled, that is enough to perform
host record search using ip
List of IP instances case:
ipvXaddrs is going to be filled with ips content,
... | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L527-L554 |
infobloxopen/infoblox-client | infoblox_client/objects.py | FixedAddressV6.mac | def mac(self, mac):
"""Set mac and duid fields
To have common interface with FixedAddress accept mac address
and set duid as a side effect.
'mac' was added to _shadow_fields to prevent sending it out over wapi.
"""
self._mac = mac
if mac:
self.duid = ... | python | def mac(self, mac):
"""Set mac and duid fields
To have common interface with FixedAddress accept mac address
and set duid as a side effect.
'mac' was added to _shadow_fields to prevent sending it out over wapi.
"""
self._mac = mac
if mac:
self.duid = ... | Set mac and duid fields
To have common interface with FixedAddress accept mac address
and set duid as a side effect.
'mac' was added to _shadow_fields to prevent sending it out over wapi. | https://github.com/infobloxopen/infoblox-client/blob/edeec62db1935784c728731b2ae7cf0fcc9bf84d/infoblox_client/objects.py#L821-L832 |
cf-platform-eng/tile-generator | tile_generator/template.py | render_property | def render_property(property):
"""Render a property for bosh manifest, according to its type."""
# This ain't the prettiest thing, but it should get the job done.
# I don't think we have anything more elegant available at bosh-manifest-generation time.
# See https://docs.pivotal.io/partners/product-template-referen... | python | def render_property(property):
"""Render a property for bosh manifest, according to its type."""
# This ain't the prettiest thing, but it should get the job done.
# I don't think we have anything more elegant available at bosh-manifest-generation time.
# See https://docs.pivotal.io/partners/product-template-referen... | Render a property for bosh manifest, according to its type. | https://github.com/cf-platform-eng/tile-generator/blob/56b602334edb38639bc7e01b1e9e68e43f9e6828/tile_generator/template.py#L152-L170 |
h2non/filetype.py | filetype/match.py | match | def match(obj, matchers=TYPES):
"""
Matches the given input againts the available
file type matchers.
Args:
obj: path to file, bytes or bytearray.
Returns:
Type instance if type matches. Otherwise None.
Raises:
TypeError: if obj is not a supported type.
"""
buf... | python | def match(obj, matchers=TYPES):
"""
Matches the given input againts the available
file type matchers.
Args:
obj: path to file, bytes or bytearray.
Returns:
Type instance if type matches. Otherwise None.
Raises:
TypeError: if obj is not a supported type.
"""
buf... | Matches the given input againts the available
file type matchers.
Args:
obj: path to file, bytes or bytearray.
Returns:
Type instance if type matches. Otherwise None.
Raises:
TypeError: if obj is not a supported type. | https://github.com/h2non/filetype.py/blob/37e7fd1a9eed1a9eab55ac43f62da98f10970675/filetype/match.py#L14-L34 |
h2non/filetype.py | filetype/utils.py | signature | def signature(array):
"""
Returns the first 262 bytes of the given bytearray
as part of the file header signature.
Args:
array: bytearray to extract the header signature.
Returns:
First 262 bytes of the file content as bytearray type.
"""
length = len(array)
index = _NU... | python | def signature(array):
"""
Returns the first 262 bytes of the given bytearray
as part of the file header signature.
Args:
array: bytearray to extract the header signature.
Returns:
First 262 bytes of the file content as bytearray type.
"""
length = len(array)
index = _NU... | Returns the first 262 bytes of the given bytearray
as part of the file header signature.
Args:
array: bytearray to extract the header signature.
Returns:
First 262 bytes of the file content as bytearray type. | https://github.com/h2non/filetype.py/blob/37e7fd1a9eed1a9eab55ac43f62da98f10970675/filetype/utils.py#L21-L35 |
h2non/filetype.py | filetype/utils.py | get_bytes | def get_bytes(obj):
"""
Infers the input type and reads the first 262 bytes,
returning a sliced bytearray.
Args:
obj: path to readable, file, bytes or bytearray.
Returns:
First 262 bytes of the file content as bytearray type.
Raises:
TypeError: if obj is not a supporte... | python | def get_bytes(obj):
"""
Infers the input type and reads the first 262 bytes,
returning a sliced bytearray.
Args:
obj: path to readable, file, bytes or bytearray.
Returns:
First 262 bytes of the file content as bytearray type.
Raises:
TypeError: if obj is not a supporte... | Infers the input type and reads the first 262 bytes,
returning a sliced bytearray.
Args:
obj: path to readable, file, bytes or bytearray.
Returns:
First 262 bytes of the file content as bytearray type.
Raises:
TypeError: if obj is not a supported type. | https://github.com/h2non/filetype.py/blob/37e7fd1a9eed1a9eab55ac43f62da98f10970675/filetype/utils.py#L38-L72 |
h2non/filetype.py | filetype/filetype.py | get_type | def get_type(mime=None, ext=None):
"""
Returns the file type instance searching by
MIME type or file extension.
Args:
ext: file extension string. E.g: jpg, png, mp4, mp3
mime: MIME string. E.g: image/jpeg, video/mpeg
Returns:
The matched file type instance. Otherwise None.
... | python | def get_type(mime=None, ext=None):
"""
Returns the file type instance searching by
MIME type or file extension.
Args:
ext: file extension string. E.g: jpg, png, mp4, mp3
mime: MIME string. E.g: image/jpeg, video/mpeg
Returns:
The matched file type instance. Otherwise None.
... | Returns the file type instance searching by
MIME type or file extension.
Args:
ext: file extension string. E.g: jpg, png, mp4, mp3
mime: MIME string. E.g: image/jpeg, video/mpeg
Returns:
The matched file type instance. Otherwise None. | https://github.com/h2non/filetype.py/blob/37e7fd1a9eed1a9eab55ac43f62da98f10970675/filetype/filetype.py#L67-L82 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail.open | def open(self, encoding=None):
"""Opens the file with the appropriate call"""
try:
if IS_GZIPPED_FILE.search(self._filename):
_file = gzip.open(self._filename, 'rb')
else:
if encoding:
_file = io.open(self._filename, 'r', encodi... | python | def open(self, encoding=None):
"""Opens the file with the appropriate call"""
try:
if IS_GZIPPED_FILE.search(self._filename):
_file = gzip.open(self._filename, 'rb')
else:
if encoding:
_file = io.open(self._filename, 'r', encodi... | Opens the file with the appropriate call | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L79-L96 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail.close | def close(self):
"""Closes all currently open file pointers"""
if not self.active:
return
self.active = False
if self._file:
self._file.close()
self._sincedb_update_position(force_update=True)
if self._current_event:
event = '\n'.... | python | def close(self):
"""Closes all currently open file pointers"""
if not self.active:
return
self.active = False
if self._file:
self._file.close()
self._sincedb_update_position(force_update=True)
if self._current_event:
event = '\n'.... | Closes all currently open file pointers | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L98-L111 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail._buffer_extract | def _buffer_extract(self, data):
"""
Extract takes an arbitrary string of input data and returns an array of
tokenized entities, provided there were any available to extract. This
makes for easy processing of datagrams using a pattern like:
tokenizer.extract(data).map { |enti... | python | def _buffer_extract(self, data):
"""
Extract takes an arbitrary string of input data and returns an array of
tokenized entities, provided there were any available to extract. This
makes for easy processing of datagrams using a pattern like:
tokenizer.extract(data).map { |enti... | Extract takes an arbitrary string of input data and returns an array of
tokenized entities, provided there were any available to extract. This
makes for easy processing of datagrams using a pattern like:
tokenizer.extract(data).map { |entity| Decode(entity) }.each do ... | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L130-L184 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail._ensure_file_is_good | def _ensure_file_is_good(self, current_time):
"""Every N seconds, ensures that the file we are tailing is the file we expect to be tailing"""
if self._last_file_mapping_update and current_time - self._last_file_mapping_update <= self._stat_interval:
return
self._last_file_mapping_up... | python | def _ensure_file_is_good(self, current_time):
"""Every N seconds, ensures that the file we are tailing is the file we expect to be tailing"""
if self._last_file_mapping_update and current_time - self._last_file_mapping_update <= self._stat_interval:
return
self._last_file_mapping_up... | Every N seconds, ensures that the file we are tailing is the file we expect to be tailing | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L197-L232 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail._run_pass | def _run_pass(self):
"""Read lines from a file and performs a callback against them"""
while True:
try:
data = self._file.read(4096)
except IOError, e:
if e.errno == errno.ESTALE:
self.active = False
return F... | python | def _run_pass(self):
"""Read lines from a file and performs a callback against them"""
while True:
try:
data = self._file.read(4096)
except IOError, e:
if e.errno == errno.ESTALE:
self.active = False
return F... | Read lines from a file and performs a callback against them | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L234-L273 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail._sincedb_init | def _sincedb_init(self):
"""Initializes the sincedb schema in an sqlite db"""
if not self._sincedb_path:
return
if not os.path.exists(self._sincedb_path):
self._log_debug('initializing sincedb sqlite schema')
conn = sqlite3.connect(self._sincedb_path, isolati... | python | def _sincedb_init(self):
"""Initializes the sincedb schema in an sqlite db"""
if not self._sincedb_path:
return
if not os.path.exists(self._sincedb_path):
self._log_debug('initializing sincedb sqlite schema')
conn = sqlite3.connect(self._sincedb_path, isolati... | Initializes the sincedb schema in an sqlite db | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L381-L396 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail._sincedb_update_position | def _sincedb_update_position(self, lines=0, force_update=False):
"""Retrieves the starting position from the sincedb sql db for a given file
Returns a boolean representing whether or not it updated the record
"""
if not self._sincedb_path:
return False
self._line_cou... | python | def _sincedb_update_position(self, lines=0, force_update=False):
"""Retrieves the starting position from the sincedb sql db for a given file
Returns a boolean representing whether or not it updated the record
"""
if not self._sincedb_path:
return False
self._line_cou... | Retrieves the starting position from the sincedb sql db for a given file
Returns a boolean representing whether or not it updated the record | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L398-L441 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail._sincedb_start_position | def _sincedb_start_position(self):
"""Retrieves the starting position from the sincedb sql db
for a given file
"""
if not self._sincedb_path:
return None
self._sincedb_init()
self._log_debug('retrieving start_position from sincedb')
conn = sqlite3.con... | python | def _sincedb_start_position(self):
"""Retrieves the starting position from the sincedb sql db
for a given file
"""
if not self._sincedb_path:
return None
self._sincedb_init()
self._log_debug('retrieving start_position from sincedb')
conn = sqlite3.con... | Retrieves the starting position from the sincedb sql db
for a given file | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L443-L463 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail._update_file | def _update_file(self, seek_to_end=True):
"""Open the file for tailing"""
try:
self.close()
self._file = self.open()
except IOError:
pass
else:
if not self._file:
return
self.active = True
try:
... | python | def _update_file(self, seek_to_end=True):
"""Open the file for tailing"""
try:
self.close()
self._file = self.open()
except IOError:
pass
else:
if not self._file:
return
self.active = True
try:
... | Open the file for tailing | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L465-L492 |
python-beaver/python-beaver | beaver/worker/tail.py | Tail.tail | def tail(self, fname, encoding, window, position=None):
"""Read last N lines from file fname."""
if window <= 0:
raise ValueError('invalid window %r' % window)
encodings = ENCODINGS
if encoding:
encodings = [encoding] + ENCODINGS
for enc in encodings:
... | python | def tail(self, fname, encoding, window, position=None):
"""Read last N lines from file fname."""
if window <= 0:
raise ValueError('invalid window %r' % window)
encodings = ENCODINGS
if encoding:
encodings = [encoding] + ENCODINGS
for enc in encodings:
... | Read last N lines from file fname. | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail.py#L494-L515 |
python-beaver/python-beaver | beaver/transports/__init__.py | create_transport | def create_transport(beaver_config, logger):
"""Creates and returns a transport object"""
transport_str = beaver_config.get('transport')
if '.' not in transport_str:
# allow simple names like 'redis' to load a beaver built-in transport
module_path = 'beaver.transports.%s_transport' % transpo... | python | def create_transport(beaver_config, logger):
"""Creates and returns a transport object"""
transport_str = beaver_config.get('transport')
if '.' not in transport_str:
# allow simple names like 'redis' to load a beaver built-in transport
module_path = 'beaver.transports.%s_transport' % transpo... | Creates and returns a transport object | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/__init__.py#L4-L22 |
python-beaver/python-beaver | beaver/worker/tail_manager.py | TailManager.listdir | def listdir(self):
"""HACK around not having a beaver_config stanza
TODO: Convert this to a glob"""
ls = os.listdir(self._folder)
return [x for x in ls if os.path.splitext(x)[1][1:] == "log"] | python | def listdir(self):
"""HACK around not having a beaver_config stanza
TODO: Convert this to a glob"""
ls = os.listdir(self._folder)
return [x for x in ls if os.path.splitext(x)[1][1:] == "log"] | HACK around not having a beaver_config stanza
TODO: Convert this to a glob | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail_manager.py#L34-L38 |
python-beaver/python-beaver | beaver/worker/tail_manager.py | TailManager.update_files | def update_files(self):
"""Ensures all files are properly loaded.
Detects new files, file removals, file rotation, and truncation.
On non-linux platforms, it will also manually reload the file for tailing.
Note that this hack is necessary because EOF is cached on BSD systems.
"""... | python | def update_files(self):
"""Ensures all files are properly loaded.
Detects new files, file removals, file rotation, and truncation.
On non-linux platforms, it will also manually reload the file for tailing.
Note that this hack is necessary because EOF is cached on BSD systems.
"""... | Ensures all files are properly loaded.
Detects new files, file removals, file rotation, and truncation.
On non-linux platforms, it will also manually reload the file for tailing.
Note that this hack is necessary because EOF is cached on BSD systems. | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail_manager.py#L85-L125 |
python-beaver/python-beaver | beaver/worker/tail_manager.py | TailManager.close | def close(self, signalnum=None, frame=None):
self._running = False
"""Closes all currently open Tail objects"""
self._log_debug("Closing all tail objects")
self._active = False
for fid in self._tails:
self._tails[fid].close()
for n in range(0,self._number_of_c... | python | def close(self, signalnum=None, frame=None):
self._running = False
"""Closes all currently open Tail objects"""
self._log_debug("Closing all tail objects")
self._active = False
for fid in self._tails:
self._tails[fid].close()
for n in range(0,self._number_of_c... | Closes all currently open Tail objects | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/worker/tail_manager.py#L127-L138 |
python-beaver/python-beaver | beaver/utils.py | eglob | def eglob(path, exclude=None):
"""Like glob.glob, but supports "/path/**/{a,b,c}.txt" lookup"""
fi = itertools.chain.from_iterable
paths = list(fi(glob2.iglob(d) for d in expand_paths(path)))
if exclude:
cached_regex = cached_regices.get(exclude, None)
if not cached_regex:
ca... | python | def eglob(path, exclude=None):
"""Like glob.glob, but supports "/path/**/{a,b,c}.txt" lookup"""
fi = itertools.chain.from_iterable
paths = list(fi(glob2.iglob(d) for d in expand_paths(path)))
if exclude:
cached_regex = cached_regices.get(exclude, None)
if not cached_regex:
ca... | Like glob.glob, but supports "/path/**/{a,b,c}.txt" lookup | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/utils.py#L134-L144 |
python-beaver/python-beaver | beaver/utils.py | expand_paths | def expand_paths(path):
"""When given a path with brackets, expands it to return all permutations
of the path with expanded brackets, similar to ant.
>>> expand_paths('../{a,b}/{c,d}')
['../a/c', '../a/d', '../b/c', '../b/d']
>>> expand_paths('../{a,b}/{a,b}.py')
['../a/a.py', '.... | python | def expand_paths(path):
"""When given a path with brackets, expands it to return all permutations
of the path with expanded brackets, similar to ant.
>>> expand_paths('../{a,b}/{c,d}')
['../a/c', '../a/d', '../b/c', '../b/d']
>>> expand_paths('../{a,b}/{a,b}.py')
['../a/a.py', '.... | When given a path with brackets, expands it to return all permutations
of the path with expanded brackets, similar to ant.
>>> expand_paths('../{a,b}/{c,d}')
['../a/c', '../a/d', '../b/c', '../b/d']
>>> expand_paths('../{a,b}/{a,b}.py')
['../a/a.py', '../a/b.py', '../b/a.py', '../b/b... | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/utils.py#L147-L171 |
python-beaver/python-beaver | beaver/utils.py | multiline_merge | def multiline_merge(lines, current_event, re_after, re_before):
""" Merge multi-line events based.
Some event (like Python trackback or Java stracktrace) spawn
on multiple line. This method will merge them using two
regular expression: regex_after and regex_before.
If a line match ... | python | def multiline_merge(lines, current_event, re_after, re_before):
""" Merge multi-line events based.
Some event (like Python trackback or Java stracktrace) spawn
on multiple line. This method will merge them using two
regular expression: regex_after and regex_before.
If a line match ... | Merge multi-line events based.
Some event (like Python trackback or Java stracktrace) spawn
on multiple line. This method will merge them using two
regular expression: regex_after and regex_before.
If a line match re_after, it will be merged with next line.
If a line match re_... | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/utils.py#L180-L210 |
python-beaver/python-beaver | beaver/ssh_tunnel.py | create_ssh_tunnel | def create_ssh_tunnel(beaver_config, logger=None):
"""Returns a BeaverSshTunnel object if the current config requires us to"""
if not beaver_config.use_ssh_tunnel():
return None
logger.info("Proxying transport using through local ssh tunnel")
return BeaverSshTunnel(beaver_config, logger=logger) | python | def create_ssh_tunnel(beaver_config, logger=None):
"""Returns a BeaverSshTunnel object if the current config requires us to"""
if not beaver_config.use_ssh_tunnel():
return None
logger.info("Proxying transport using through local ssh tunnel")
return BeaverSshTunnel(beaver_config, logger=logger) | Returns a BeaverSshTunnel object if the current config requires us to | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/ssh_tunnel.py#L10-L16 |
python-beaver/python-beaver | beaver/ssh_tunnel.py | BeaverSubprocess.poll | def poll(self):
"""Poll attached subprocess until it is available"""
if self._subprocess is not None:
self._subprocess.poll()
time.sleep(self._beaver_config.get('subprocess_poll_sleep')) | python | def poll(self):
"""Poll attached subprocess until it is available"""
if self._subprocess is not None:
self._subprocess.poll()
time.sleep(self._beaver_config.get('subprocess_poll_sleep')) | Poll attached subprocess until it is available | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/ssh_tunnel.py#L43-L48 |
python-beaver/python-beaver | beaver/ssh_tunnel.py | BeaverSubprocess.close | def close(self):
"""Close child subprocess"""
if self._subprocess is not None:
os.killpg(self._subprocess.pid, signal.SIGTERM)
self._subprocess = None | python | def close(self):
"""Close child subprocess"""
if self._subprocess is not None:
os.killpg(self._subprocess.pid, signal.SIGTERM)
self._subprocess = None | Close child subprocess | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/ssh_tunnel.py#L50-L54 |
python-beaver/python-beaver | beaver/transports/mqtt_transport.py | MqttTransport.callback | def callback(self, filename, lines, **kwargs):
"""publishes lines one by one to the given topic"""
timestamp = self.get_timestamp(**kwargs)
if kwargs.get('timestamp', False):
del kwargs['timestamp']
for line in lines:
try:
import warnings
... | python | def callback(self, filename, lines, **kwargs):
"""publishes lines one by one to the given topic"""
timestamp = self.get_timestamp(**kwargs)
if kwargs.get('timestamp', False):
del kwargs['timestamp']
for line in lines:
try:
import warnings
... | publishes lines one by one to the given topic | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/mqtt_transport.py#L33-L49 |
python-beaver/python-beaver | beaver/unicode_dammit.py | _to_unicode | def _to_unicode(self, data, encoding, errors='strict'):
'''Given a string and its encoding, decodes the string into Unicode.
%encoding is a string recognized by encodings.aliases'''
# strip Byte Order Mark (if present)
if (len(data) >= 4) and (data[:2] == '\xfe\xff') and (data[2:4] != '\x00\x00'):
... | python | def _to_unicode(self, data, encoding, errors='strict'):
'''Given a string and its encoding, decodes the string into Unicode.
%encoding is a string recognized by encodings.aliases'''
# strip Byte Order Mark (if present)
if (len(data) >= 4) and (data[:2] == '\xfe\xff') and (data[2:4] != '\x00\x00'):
... | Given a string and its encoding, decodes the string into Unicode.
%encoding is a string recognized by encodings.aliases | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/unicode_dammit.py#L38-L59 |
python-beaver/python-beaver | beaver/transports/stomp_transport.py | StompTransport.callback | def callback(self, filename, lines, **kwargs):
"""publishes lines one by one to the given topic"""
timestamp = self.get_timestamp(**kwargs)
if kwargs.get('timestamp', False):
del kwargs['timestamp']
for line in lines:
try:
import warnings... | python | def callback(self, filename, lines, **kwargs):
"""publishes lines one by one to the given topic"""
timestamp = self.get_timestamp(**kwargs)
if kwargs.get('timestamp', False):
del kwargs['timestamp']
for line in lines:
try:
import warnings... | publishes lines one by one to the given topic | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/stomp_transport.py#L21-L42 |
python-beaver/python-beaver | beaver/transports/stomp_transport.py | StompTransport.reconnect | def reconnect(self):
"""Allows reconnection from when a handled
TransportException is thrown"""
try:
self.conn.close()
except Exception,e:
self.logger.warn(e)
self.createConnection()
return True | python | def reconnect(self):
"""Allows reconnection from when a handled
TransportException is thrown"""
try:
self.conn.close()
except Exception,e:
self.logger.warn(e)
self.createConnection()
return True | Allows reconnection from when a handled
TransportException is thrown | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/stomp_transport.py#L64-L74 |
python-beaver/python-beaver | beaver/transports/redis_transport.py | RedisTransport._check_connections | def _check_connections(self):
"""Checks if all configured redis servers are reachable"""
for server in self._servers:
if self._is_reachable(server):
server['down_until'] = 0
else:
server['down_until'] = time.time() + 5 | python | def _check_connections(self):
"""Checks if all configured redis servers are reachable"""
for server in self._servers:
if self._is_reachable(server):
server['down_until'] = 0
else:
server['down_until'] = time.time() + 5 | Checks if all configured redis servers are reachable | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/redis_transport.py#L38-L45 |
python-beaver/python-beaver | beaver/transports/redis_transport.py | RedisTransport._is_reachable | def _is_reachable(self, server):
"""Checks if the given redis server is reachable"""
try:
server['redis'].ping()
return True
except UserWarning:
self._logger.warn('Cannot reach redis server: ' + server['url'])
except Exception:
self._logge... | python | def _is_reachable(self, server):
"""Checks if the given redis server is reachable"""
try:
server['redis'].ping()
return True
except UserWarning:
self._logger.warn('Cannot reach redis server: ' + server['url'])
except Exception:
self._logge... | Checks if the given redis server is reachable | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/redis_transport.py#L47-L58 |
python-beaver/python-beaver | beaver/transports/redis_transport.py | RedisTransport.invalidate | def invalidate(self):
"""Invalidates the current transport and disconnects all redis connections"""
super(RedisTransport, self).invalidate()
for server in self._servers:
server['redis'].connection_pool.disconnect()
return False | python | def invalidate(self):
"""Invalidates the current transport and disconnects all redis connections"""
super(RedisTransport, self).invalidate()
for server in self._servers:
server['redis'].connection_pool.disconnect()
return False | Invalidates the current transport and disconnects all redis connections | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/redis_transport.py#L63-L69 |
python-beaver/python-beaver | beaver/transports/redis_transport.py | RedisTransport.callback | def callback(self, filename, lines, **kwargs):
"""Sends log lines to redis servers"""
self._logger.debug('Redis transport called')
timestamp = self.get_timestamp(**kwargs)
if kwargs.get('timestamp', False):
del kwargs['timestamp']
namespaces = self._beaver_config.g... | python | def callback(self, filename, lines, **kwargs):
"""Sends log lines to redis servers"""
self._logger.debug('Redis transport called')
timestamp = self.get_timestamp(**kwargs)
if kwargs.get('timestamp', False):
del kwargs['timestamp']
namespaces = self._beaver_config.g... | Sends log lines to redis servers | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/redis_transport.py#L71-L112 |
python-beaver/python-beaver | beaver/transports/redis_transport.py | RedisTransport._get_next_server | def _get_next_server(self):
"""Returns a valid redis server or raises a TransportException"""
current_try = 0
max_tries = len(self._servers)
while current_try < max_tries:
server_index = self._raise_server_index()
server = self._servers[server_index]
... | python | def _get_next_server(self):
"""Returns a valid redis server or raises a TransportException"""
current_try = 0
max_tries = len(self._servers)
while current_try < max_tries:
server_index = self._raise_server_index()
server = self._servers[server_index]
... | Returns a valid redis server or raises a TransportException | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/redis_transport.py#L114-L144 |
python-beaver/python-beaver | beaver/transports/redis_transport.py | RedisTransport._raise_server_index | def _raise_server_index(self):
"""Round robin magic: Raises the current redis server index and returns it"""
self._current_server_index = (self._current_server_index + 1) % len(self._servers)
return self._current_server_index | python | def _raise_server_index(self):
"""Round robin magic: Raises the current redis server index and returns it"""
self._current_server_index = (self._current_server_index + 1) % len(self._servers)
return self._current_server_index | Round robin magic: Raises the current redis server index and returns it | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/redis_transport.py#L146-L151 |
python-beaver/python-beaver | beaver/transports/redis_transport.py | RedisTransport.valid | def valid(self):
"""Returns whether or not the transport can send data to any redis server"""
valid_servers = 0
for server in self._servers:
if server['down_until'] <= time.time():
valid_servers += 1
return valid_servers > 0 | python | def valid(self):
"""Returns whether or not the transport can send data to any redis server"""
valid_servers = 0
for server in self._servers:
if server['down_until'] <= time.time():
valid_servers += 1
return valid_servers > 0 | Returns whether or not the transport can send data to any redis server | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/redis_transport.py#L154-L162 |
python-beaver/python-beaver | beaver/transports/kafka_transport.py | KafkaTransport.callback | def callback(self, filename, lines, **kwargs):
"""publishes lines one by one to the given topic"""
timestamp = self.get_timestamp(**kwargs)
if kwargs.get('timestamp', False):
del kwargs['timestamp']
for line in lines:
try:
import warnings
... | python | def callback(self, filename, lines, **kwargs):
"""publishes lines one by one to the given topic"""
timestamp = self.get_timestamp(**kwargs)
if kwargs.get('timestamp', False):
del kwargs['timestamp']
for line in lines:
try:
import warnings
... | publishes lines one by one to the given topic | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/kafka_transport.py#L52-L79 |
python-beaver/python-beaver | beaver/transports/base_transport.py | BaseTransport.format | def format(self, filename, line, timestamp, **kwargs):
"""Returns a formatted log line"""
line = unicode(line.encode("utf-8"), "utf-8", errors="ignore")
formatter = self._beaver_config.get_field('format', filename)
if formatter not in self._formatters:
formatter = self._defau... | python | def format(self, filename, line, timestamp, **kwargs):
"""Returns a formatted log line"""
line = unicode(line.encode("utf-8"), "utf-8", errors="ignore")
formatter = self._beaver_config.get_field('format', filename)
if formatter not in self._formatters:
formatter = self._defau... | Returns a formatted log line | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/base_transport.py#L117-L142 |
python-beaver/python-beaver | beaver/transports/base_transport.py | BaseTransport.get_timestamp | def get_timestamp(self, **kwargs):
"""Retrieves the timestamp for a given set of data"""
timestamp = kwargs.get('timestamp')
if not timestamp:
now = datetime.datetime.utcnow()
timestamp = now.strftime("%Y-%m-%dT%H:%M:%S") + ".%03d" % (now.microsecond / 1000) + "Z"
... | python | def get_timestamp(self, **kwargs):
"""Retrieves the timestamp for a given set of data"""
timestamp = kwargs.get('timestamp')
if not timestamp:
now = datetime.datetime.utcnow()
timestamp = now.strftime("%Y-%m-%dT%H:%M:%S") + ".%03d" % (now.microsecond / 1000) + "Z"
... | Retrieves the timestamp for a given set of data | https://github.com/python-beaver/python-beaver/blob/93941e968016c5a962dffed9e7a9f6dc1d23236c/beaver/transports/base_transport.py#L144-L151 |
gqmelo/exec-wrappers | exec_wrappers/create_wrappers.py | _make_executable | def _make_executable(path):
"""Make the file at path executable."""
os.chmod(path, os.stat(path).st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH) | python | def _make_executable(path):
"""Make the file at path executable."""
os.chmod(path, os.stat(path).st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH) | Make the file at path executable. | https://github.com/gqmelo/exec-wrappers/blob/0faf892a103cf03d005f1dbdc71ca52d279b4e3b/exec_wrappers/create_wrappers.py#L300-L302 |
cmap/cmapPy | cmapPy/pandasGEXpress/subset.py | build_parser | def build_parser():
"""Build argument parser."""
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
# Required args
parser.add_argument("--in_path", "-i", required=True,
help="file p... | python | def build_parser():
"""Build argument parser."""
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
# Required args
parser.add_argument("--in_path", "-i", required=True,
help="file p... | Build argument parser. | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/subset.py#L28-L49 |
cmap/cmapPy | cmapPy/pandasGEXpress/subset.py | subset_main | def subset_main(args):
""" Separate method from main() in order to make testing easier and to
enable command-line access. """
# Read in each of the command line arguments
rid = _read_arg(args.rid)
cid = _read_arg(args.cid)
exclude_rid = _read_arg(args.exclude_rid)
exclude_cid = _read_arg(ar... | python | def subset_main(args):
""" Separate method from main() in order to make testing easier and to
enable command-line access. """
# Read in each of the command line arguments
rid = _read_arg(args.rid)
cid = _read_arg(args.cid)
exclude_rid = _read_arg(args.exclude_rid)
exclude_cid = _read_arg(ar... | Separate method from main() in order to make testing easier and to
enable command-line access. | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/subset.py#L59-L91 |
cmap/cmapPy | cmapPy/pandasGEXpress/subset.py | _read_arg | def _read_arg(arg):
"""
If arg is a list with 1 element that corresponds to a valid file path, use
set_io.grp to read the grp file. Otherwise, check that arg is a list of strings.
Args:
arg (list or None)
Returns:
arg_out (list or None)
"""
# If arg is None, just return it... | python | def _read_arg(arg):
"""
If arg is a list with 1 element that corresponds to a valid file path, use
set_io.grp to read the grp file. Otherwise, check that arg is a list of strings.
Args:
arg (list or None)
Returns:
arg_out (list or None)
"""
# If arg is None, just return it... | If arg is a list with 1 element that corresponds to a valid file path, use
set_io.grp to read the grp file. Otherwise, check that arg is a list of strings.
Args:
arg (list or None)
Returns:
arg_out (list or None) | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/subset.py#L94-L121 |
cmap/cmapPy | cmapPy/math/fast_cov.py | fast_cov | def fast_cov(x, y=None, destination=None):
"""calculate the covariance matrix for the columns of x (MxN), or optionally, the covariance matrix between the
columns of x and and the columns of y (MxP). (In the language of statistics, the columns are variables, the rows
are observations).
Args:
x... | python | def fast_cov(x, y=None, destination=None):
"""calculate the covariance matrix for the columns of x (MxN), or optionally, the covariance matrix between the
columns of x and and the columns of y (MxP). (In the language of statistics, the columns are variables, the rows
are observations).
Args:
x... | calculate the covariance matrix for the columns of x (MxN), or optionally, the covariance matrix between the
columns of x and and the columns of y (MxP). (In the language of statistics, the columns are variables, the rows
are observations).
Args:
x (numpy array-like) MxN in shape
y (numpy ... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/math/fast_cov.py#L9-L41 |
cmap/cmapPy | cmapPy/set_io/gmt.py | read | def read(file_path):
""" Read a gmt file at the path specified by file_path.
Args:
file_path (string): path to gmt file
Returns:
gmt (GMT object): list of dicts, where each dict corresponds to one
line of the GMT file
"""
# Read in file
actual_file_path = os.path.e... | python | def read(file_path):
""" Read a gmt file at the path specified by file_path.
Args:
file_path (string): path to gmt file
Returns:
gmt (GMT object): list of dicts, where each dict corresponds to one
line of the GMT file
"""
# Read in file
actual_file_path = os.path.e... | Read a gmt file at the path specified by file_path.
Args:
file_path (string): path to gmt file
Returns:
gmt (GMT object): list of dicts, where each dict corresponds to one
line of the GMT file | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/set_io/gmt.py#L24-L73 |
cmap/cmapPy | cmapPy/set_io/gmt.py | verify_gmt_integrity | def verify_gmt_integrity(gmt):
""" Make sure that set ids are unique.
Args:
gmt (GMT object): list of dicts
Returns:
None
"""
# Verify that set ids are unique
set_ids = [d[SET_IDENTIFIER_FIELD] for d in gmt]
assert len(set(set_ids)) == len(set_ids), (
"Set identif... | python | def verify_gmt_integrity(gmt):
""" Make sure that set ids are unique.
Args:
gmt (GMT object): list of dicts
Returns:
None
"""
# Verify that set ids are unique
set_ids = [d[SET_IDENTIFIER_FIELD] for d in gmt]
assert len(set(set_ids)) == len(set_ids), (
"Set identif... | Make sure that set ids are unique.
Args:
gmt (GMT object): list of dicts
Returns:
None | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/set_io/gmt.py#L76-L90 |
cmap/cmapPy | cmapPy/set_io/gmt.py | write | def write(gmt, out_path):
""" Write a GMT to a text file.
Args:
gmt (GMT object): list of dicts
out_path (string): output path
Returns:
None
"""
with open(out_path, 'w') as f:
for _, each_dict in enumerate(gmt):
f.write(each_dict[SET_IDENTIFIER_FIELD] +... | python | def write(gmt, out_path):
""" Write a GMT to a text file.
Args:
gmt (GMT object): list of dicts
out_path (string): output path
Returns:
None
"""
with open(out_path, 'w') as f:
for _, each_dict in enumerate(gmt):
f.write(each_dict[SET_IDENTIFIER_FIELD] +... | Write a GMT to a text file.
Args:
gmt (GMT object): list of dicts
out_path (string): output path
Returns:
None | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/set_io/gmt.py#L93-L109 |
cmap/cmapPy | cmapPy/pandasGEXpress/diff_gctoo.py | diff_gctoo | def diff_gctoo(gctoo, plate_control=True, group_field='pert_type', group_val='ctl_vehicle',
diff_method="robust_z", upper_diff_thresh=10, lower_diff_thresh=-10):
''' Converts a matrix of values (e.g. gene expression, viability, etc.)
into a matrix of differential values.
Args:
df (pandas... | python | def diff_gctoo(gctoo, plate_control=True, group_field='pert_type', group_val='ctl_vehicle',
diff_method="robust_z", upper_diff_thresh=10, lower_diff_thresh=-10):
''' Converts a matrix of values (e.g. gene expression, viability, etc.)
into a matrix of differential values.
Args:
df (pandas... | Converts a matrix of values (e.g. gene expression, viability, etc.)
into a matrix of differential values.
Args:
df (pandas df): data to make diff_gctoo
plate_control (bool): True means calculate diff_gctoo using plate control.
False means vehicle control.
group_field (string): Metadata fiel... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/diff_gctoo.py#L18-L84 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | parse | def parse(gctx_file_path, convert_neg_666=True, rid=None, cid=None,
ridx=None, cidx=None, row_meta_only=False, col_meta_only=False, make_multiindex=False):
"""
Primary method of script. Reads in path to a gctx file and parses into GCToo object.
Input:
Mandatory:
- gctx_file_path (... | python | def parse(gctx_file_path, convert_neg_666=True, rid=None, cid=None,
ridx=None, cidx=None, row_meta_only=False, col_meta_only=False, make_multiindex=False):
"""
Primary method of script. Reads in path to a gctx file and parses into GCToo object.
Input:
Mandatory:
- gctx_file_path (... | Primary method of script. Reads in path to a gctx file and parses into GCToo object.
Input:
Mandatory:
- gctx_file_path (str): full path to gctx file you want to parse.
Optional:
- convert_neg_666 (bool): whether to convert -666 values to numpy.nan or not
(see Note belo... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L23-L126 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | check_and_order_id_inputs | def check_and_order_id_inputs(rid, ridx, cid, cidx, row_meta_df, col_meta_df):
"""
Makes sure that (if entered) id inputs entered are of one type (string id or index)
Input:
- rid (list or None): if not None, a list of rids
- ridx (list or None): if not None, a list of indexes
- cid ... | python | def check_and_order_id_inputs(rid, ridx, cid, cidx, row_meta_df, col_meta_df):
"""
Makes sure that (if entered) id inputs entered are of one type (string id or index)
Input:
- rid (list or None): if not None, a list of rids
- ridx (list or None): if not None, a list of indexes
- cid ... | Makes sure that (if entered) id inputs entered are of one type (string id or index)
Input:
- rid (list or None): if not None, a list of rids
- ridx (list or None): if not None, a list of indexes
- cid (list or None): if not None, a list of cids
- cidx (list or None): if not None, a l... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L129-L148 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | check_id_idx_exclusivity | def check_id_idx_exclusivity(id, idx):
"""
Makes sure user didn't provide both ids and idx values to subset by.
Input:
- id (list or None): if not None, a list of string id names
- idx (list or None): if not None, a list of integer id indexes
Output:
- a tuple: first element is... | python | def check_id_idx_exclusivity(id, idx):
"""
Makes sure user didn't provide both ids and idx values to subset by.
Input:
- id (list or None): if not None, a list of string id names
- idx (list or None): if not None, a list of integer id indexes
Output:
- a tuple: first element is... | Makes sure user didn't provide both ids and idx values to subset by.
Input:
- id (list or None): if not None, a list of string id names
- idx (list or None): if not None, a list of integer id indexes
Output:
- a tuple: first element is subset type, second is subset content | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L151-L172 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | get_ordered_idx | def get_ordered_idx(id_type, id_list, meta_df):
"""
Gets index values corresponding to ids to subset and orders them.
Input:
- id_type (str): either "id", "idx" or None
- id_list (list): either a list of indexes or id names
Output:
- a sorted list of indexes to subset a dimension... | python | def get_ordered_idx(id_type, id_list, meta_df):
"""
Gets index values corresponding to ids to subset and orders them.
Input:
- id_type (str): either "id", "idx" or None
- id_list (list): either a list of indexes or id names
Output:
- a sorted list of indexes to subset a dimension... | Gets index values corresponding to ids to subset and orders them.
Input:
- id_type (str): either "id", "idx" or None
- id_list (list): either a list of indexes or id names
Output:
- a sorted list of indexes to subset a dimension by | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L219-L236 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | parse_metadata_df | def parse_metadata_df(dim, meta_group, convert_neg_666):
"""
Reads in all metadata from .gctx file to pandas DataFrame
with proper GCToo specifications.
Input:
- dim (str): Dimension of metadata; either "row" or "column"
- meta_group (HDF5 group): Group from which to read metadata values... | python | def parse_metadata_df(dim, meta_group, convert_neg_666):
"""
Reads in all metadata from .gctx file to pandas DataFrame
with proper GCToo specifications.
Input:
- dim (str): Dimension of metadata; either "row" or "column"
- meta_group (HDF5 group): Group from which to read metadata values... | Reads in all metadata from .gctx file to pandas DataFrame
with proper GCToo specifications.
Input:
- dim (str): Dimension of metadata; either "row" or "column"
- meta_group (HDF5 group): Group from which to read metadata values
- convert_neg_666 (bool): whether to convert "-666" values t... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L239-L284 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | replace_666 | def replace_666(meta_df, convert_neg_666):
""" Replace -666, -666.0, and optionally "-666".
Args:
meta_df (pandas df):
convert_neg_666 (bool):
Returns:
out_df (pandas df): updated meta_df
"""
if convert_neg_666:
out_df = meta_df.replace([-666, "-666", -666.0], np.nan)... | python | def replace_666(meta_df, convert_neg_666):
""" Replace -666, -666.0, and optionally "-666".
Args:
meta_df (pandas df):
convert_neg_666 (bool):
Returns:
out_df (pandas df): updated meta_df
"""
if convert_neg_666:
out_df = meta_df.replace([-666, "-666", -666.0], np.nan)... | Replace -666, -666.0, and optionally "-666".
Args:
meta_df (pandas df):
convert_neg_666 (bool):
Returns:
out_df (pandas df): updated meta_df | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L287-L299 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | set_metadata_index_and_column_names | def set_metadata_index_and_column_names(dim, meta_df):
"""
Sets index and column names to GCTX convention.
Input:
- dim (str): Dimension of metadata to read. Must be either "row" or "col"
- meta_df (pandas.DataFrame): data frame corresponding to metadata fields
of dimension speci... | python | def set_metadata_index_and_column_names(dim, meta_df):
"""
Sets index and column names to GCTX convention.
Input:
- dim (str): Dimension of metadata to read. Must be either "row" or "col"
- meta_df (pandas.DataFrame): data frame corresponding to metadata fields
of dimension speci... | Sets index and column names to GCTX convention.
Input:
- dim (str): Dimension of metadata to read. Must be either "row" or "col"
- meta_df (pandas.DataFrame): data frame corresponding to metadata fields
of dimension specified.
Output:
None | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L302-L317 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | parse_data_df | def parse_data_df(data_dset, ridx, cidx, row_meta, col_meta):
"""
Parses in data_df from hdf5, subsetting if specified.
Input:
-data_dset (h5py dset): HDF5 dataset from which to read data_df
-ridx (list): list of indexes to subset from data_df
(may be all of them if no subsettin... | python | def parse_data_df(data_dset, ridx, cidx, row_meta, col_meta):
"""
Parses in data_df from hdf5, subsetting if specified.
Input:
-data_dset (h5py dset): HDF5 dataset from which to read data_df
-ridx (list): list of indexes to subset from data_df
(may be all of them if no subsettin... | Parses in data_df from hdf5, subsetting if specified.
Input:
-data_dset (h5py dset): HDF5 dataset from which to read data_df
-ridx (list): list of indexes to subset from data_df
(may be all of them if no subsetting)
-cidx (list): list of indexes to subset from data_df
... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L320-L345 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | get_column_metadata | def get_column_metadata(gctx_file_path, convert_neg_666=True):
"""
Opens .gctx file and returns only column metadata
Input:
Mandatory:
- gctx_file_path (str): full path to gctx file you want to parse.
Optional:
- convert_neg_666 (bool): whether to convert -666 values to num... | python | def get_column_metadata(gctx_file_path, convert_neg_666=True):
"""
Opens .gctx file and returns only column metadata
Input:
Mandatory:
- gctx_file_path (str): full path to gctx file you want to parse.
Optional:
- convert_neg_666 (bool): whether to convert -666 values to num... | Opens .gctx file and returns only column metadata
Input:
Mandatory:
- gctx_file_path (str): full path to gctx file you want to parse.
Optional:
- convert_neg_666 (bool): whether to convert -666 values to num
Output:
- col_meta (pandas DataFrame): a DataFrame of all col... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L348-L368 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gctx.py | get_row_metadata | def get_row_metadata(gctx_file_path, convert_neg_666=True):
"""
Opens .gctx file and returns only row metadata
Input:
Mandatory:
- gctx_file_path (str): full path to gctx file you want to parse.
Optional:
- convert_neg_666 (bool): whether to convert -666 values to num
... | python | def get_row_metadata(gctx_file_path, convert_neg_666=True):
"""
Opens .gctx file and returns only row metadata
Input:
Mandatory:
- gctx_file_path (str): full path to gctx file you want to parse.
Optional:
- convert_neg_666 (bool): whether to convert -666 values to num
... | Opens .gctx file and returns only row metadata
Input:
Mandatory:
- gctx_file_path (str): full path to gctx file you want to parse.
Optional:
- convert_neg_666 (bool): whether to convert -666 values to num
Output:
- row_meta (pandas DataFrame): a DataFrame of all row me... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gctx.py#L371-L391 |
cmap/cmapPy | cmapPy/pandasGEXpress/GCToo.py | multi_index_df_to_component_dfs | def multi_index_df_to_component_dfs(multi_index_df, rid="rid", cid="cid"):
""" Convert a multi-index df into 3 component dfs. """
# Id level of the multiindex will become the index
rids = list(multi_index_df.index.get_level_values(rid))
cids = list(multi_index_df.columns.get_level_values(cid))
# I... | python | def multi_index_df_to_component_dfs(multi_index_df, rid="rid", cid="cid"):
""" Convert a multi-index df into 3 component dfs. """
# Id level of the multiindex will become the index
rids = list(multi_index_df.index.get_level_values(rid))
cids = list(multi_index_df.columns.get_level_values(cid))
# I... | Convert a multi-index df into 3 component dfs. | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/GCToo.py#L222-L284 |
cmap/cmapPy | cmapPy/pandasGEXpress/GCToo.py | GCToo.check_df | def check_df(self, df):
"""
Verifies that df is a pandas DataFrame instance and
that its index and column values are unique.
"""
if isinstance(df, pd.DataFrame):
if not df.index.is_unique:
repeats = df.index[df.index.duplicated()].values
... | python | def check_df(self, df):
"""
Verifies that df is a pandas DataFrame instance and
that its index and column values are unique.
"""
if isinstance(df, pd.DataFrame):
if not df.index.is_unique:
repeats = df.index[df.index.duplicated()].values
... | Verifies that df is a pandas DataFrame instance and
that its index and column values are unique. | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/GCToo.py#L125-L145 |
cmap/cmapPy | cmapPy/pandasGEXpress/GCToo.py | GCToo.id_match_check | def id_match_check(self, data_df, meta_df, dim):
"""
Verifies that id values match between:
- row case: index of data_df & index of row metadata
- col case: columns of data_df & index of column metadata
"""
if dim == "row":
if len(data_df.index) == len... | python | def id_match_check(self, data_df, meta_df, dim):
"""
Verifies that id values match between:
- row case: index of data_df & index of row metadata
- col case: columns of data_df & index of column metadata
"""
if dim == "row":
if len(data_df.index) == len... | Verifies that id values match between:
- row case: index of data_df & index of row metadata
- col case: columns of data_df & index of column metadata | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/GCToo.py#L147-L168 |
cmap/cmapPy | cmapPy/pandasGEXpress/GCToo.py | GCToo.assemble_multi_index_df | def assemble_multi_index_df(self):
"""Assembles three component dataframes into a multiindex dataframe.
Sets the result to self.multi_index_df.
IMPORTANT: Cross-section ("xs") is the best command for selecting
data. Be sure to use the flag "drop_level=False" with this command,
or... | python | def assemble_multi_index_df(self):
"""Assembles three component dataframes into a multiindex dataframe.
Sets the result to self.multi_index_df.
IMPORTANT: Cross-section ("xs") is the best command for selecting
data. Be sure to use the flag "drop_level=False" with this command,
or... | Assembles three component dataframes into a multiindex dataframe.
Sets the result to self.multi_index_df.
IMPORTANT: Cross-section ("xs") is the best command for selecting
data. Be sure to use the flag "drop_level=False" with this command,
or else the dataframe that is returned will not ... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/GCToo.py#L188-L219 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse_gct.py | parse | def parse(file_path, convert_neg_666=True, rid=None, cid=None,
ridx=None, cidx=None, row_meta_only=False, col_meta_only=False, make_multiindex=False):
"""
The main method.
Args:
- file_path (string): full path to gct(x) file you want to parse
- convert_neg_666 (bool): whether to c... | python | def parse(file_path, convert_neg_666=True, rid=None, cid=None,
ridx=None, cidx=None, row_meta_only=False, col_meta_only=False, make_multiindex=False):
"""
The main method.
Args:
- file_path (string): full path to gct(x) file you want to parse
- convert_neg_666 (bool): whether to c... | The main method.
Args:
- file_path (string): full path to gct(x) file you want to parse
- convert_neg_666 (bool): whether to convert -666 values to numpy.nan
(see Note below for more details). Default = False.
- rid (list of strings): list of row ids to specifically keep from gc... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse_gct.py#L82-L160 |
cmap/cmapPy | cmapPy/clue_api_client/gene_queries.py | are_genes_in_api | def are_genes_in_api(my_clue_api_client, gene_symbols):
"""determine if genes are present in the API
Args:
my_clue_api_client:
gene_symbols: collection of gene symbols to query the API with
Returns: set of the found gene symbols
"""
if len(gene_symbols) > 0:
query_gene_sym... | python | def are_genes_in_api(my_clue_api_client, gene_symbols):
"""determine if genes are present in the API
Args:
my_clue_api_client:
gene_symbols: collection of gene symbols to query the API with
Returns: set of the found gene symbols
"""
if len(gene_symbols) > 0:
query_gene_sym... | determine if genes are present in the API
Args:
my_clue_api_client:
gene_symbols: collection of gene symbols to query the API with
Returns: set of the found gene symbols | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/clue_api_client/gene_queries.py#L13-L34 |
cmap/cmapPy | cmapPy/pandasGEXpress/write_gct.py | write | def write(gctoo, out_fname, data_null="NaN", metadata_null="-666", filler_null="-666", data_float_format="%.4f"):
"""Write a gctoo object to a gct file.
Args:
gctoo (gctoo object)
out_fname (string): filename for output gct file
data_null (string): how to represent missing values in the... | python | def write(gctoo, out_fname, data_null="NaN", metadata_null="-666", filler_null="-666", data_float_format="%.4f"):
"""Write a gctoo object to a gct file.
Args:
gctoo (gctoo object)
out_fname (string): filename for output gct file
data_null (string): how to represent missing values in the... | Write a gctoo object to a gct file.
Args:
gctoo (gctoo object)
out_fname (string): filename for output gct file
data_null (string): how to represent missing values in the data (default = "NaN")
metadata_null (string): how to represent missing values in the metadata (default = "-666"... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/write_gct.py#L16-L51 |
cmap/cmapPy | cmapPy/pandasGEXpress/write_gct.py | write_version_and_dims | def write_version_and_dims(version, dims, f):
"""Write first two lines of gct file.
Args:
version (string): 1.3 by default
dims (list of strings): length = 4
f (file handle): handle of output file
Returns:
nothing
"""
f.write(("#" + version + "\n"))
f.write((dims... | python | def write_version_and_dims(version, dims, f):
"""Write first two lines of gct file.
Args:
version (string): 1.3 by default
dims (list of strings): length = 4
f (file handle): handle of output file
Returns:
nothing
"""
f.write(("#" + version + "\n"))
f.write((dims... | Write first two lines of gct file.
Args:
version (string): 1.3 by default
dims (list of strings): length = 4
f (file handle): handle of output file
Returns:
nothing | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/write_gct.py#L54-L65 |
cmap/cmapPy | cmapPy/pandasGEXpress/write_gct.py | write_top_half | def write_top_half(f, row_metadata_df, col_metadata_df, metadata_null, filler_null):
""" Write the top half of the gct file: top-left filler values, row metadata
headers, and top-right column metadata.
Args:
f (file handle): handle for output file
row_metadata_df (pandas df)
col_met... | python | def write_top_half(f, row_metadata_df, col_metadata_df, metadata_null, filler_null):
""" Write the top half of the gct file: top-left filler values, row metadata
headers, and top-right column metadata.
Args:
f (file handle): handle for output file
row_metadata_df (pandas df)
col_met... | Write the top half of the gct file: top-left filler values, row metadata
headers, and top-right column metadata.
Args:
f (file handle): handle for output file
row_metadata_df (pandas df)
col_metadata_df (pandas df)
metadata_null (string): how to represent missing values in the m... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/write_gct.py#L68-L102 |
cmap/cmapPy | cmapPy/pandasGEXpress/write_gct.py | write_bottom_half | def write_bottom_half(f, row_metadata_df, data_df, data_null, data_float_format, metadata_null):
""" Write the bottom half of the gct file: row metadata and data.
Args:
f (file handle): handle for output file
row_metadata_df (pandas df)
data_df (pandas df)
data_null (string): ho... | python | def write_bottom_half(f, row_metadata_df, data_df, data_null, data_float_format, metadata_null):
""" Write the bottom half of the gct file: row metadata and data.
Args:
f (file handle): handle for output file
row_metadata_df (pandas df)
data_df (pandas df)
data_null (string): ho... | Write the bottom half of the gct file: row metadata and data.
Args:
f (file handle): handle for output file
row_metadata_df (pandas df)
data_df (pandas df)
data_null (string): how to represent missing values in the data
metadata_null (string): how to represent missing values... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/write_gct.py#L105-L139 |
cmap/cmapPy | cmapPy/pandasGEXpress/write_gct.py | append_dims_and_file_extension | def append_dims_and_file_extension(fname, data_df):
"""Append dimensions and file extension to output filename.
N.B. Dimensions are cols x rows.
Args:
fname (string): output filename
data_df (pandas df)
Returns:
out_fname (string): output filename with matrix dims and .gct appen... | python | def append_dims_and_file_extension(fname, data_df):
"""Append dimensions and file extension to output filename.
N.B. Dimensions are cols x rows.
Args:
fname (string): output filename
data_df (pandas df)
Returns:
out_fname (string): output filename with matrix dims and .gct appen... | Append dimensions and file extension to output filename.
N.B. Dimensions are cols x rows.
Args:
fname (string): output filename
data_df (pandas df)
Returns:
out_fname (string): output filename with matrix dims and .gct appended | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/write_gct.py#L142-L161 |
cmap/cmapPy | cmapPy/math/robust_zscore.py | robust_zscore | def robust_zscore(mat, ctrl_mat=None, min_mad=0.1):
''' Robustly z-score a pandas df along the rows.
Args:
mat (pandas df): Matrix of data that z-scoring will be applied to
ctrl_mat (pandas df): Optional matrix from which to compute medians and MADs
(e.g. vehicle control)
min_mad (float): M... | python | def robust_zscore(mat, ctrl_mat=None, min_mad=0.1):
''' Robustly z-score a pandas df along the rows.
Args:
mat (pandas df): Matrix of data that z-scoring will be applied to
ctrl_mat (pandas df): Optional matrix from which to compute medians and MADs
(e.g. vehicle control)
min_mad (float): M... | Robustly z-score a pandas df along the rows.
Args:
mat (pandas df): Matrix of data that z-scoring will be applied to
ctrl_mat (pandas df): Optional matrix from which to compute medians and MADs
(e.g. vehicle control)
min_mad (float): Minimum MAD to threshold to; tiny MAD values will cause
... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/math/robust_zscore.py#L24-L58 |
cmap/cmapPy | cmapPy/pandasGEXpress/gct2gctx.py | gct2gctx_main | def gct2gctx_main(args):
""" Separate from main() in order to make command-line tool. """
in_gctoo = parse_gct.parse(args.filename, convert_neg_666=False)
if args.output_filepath is None:
basename = os.path.basename(args.filename)
out_name = os.path.splitext(basename)[0] + ".gctx"
else... | python | def gct2gctx_main(args):
""" Separate from main() in order to make command-line tool. """
in_gctoo = parse_gct.parse(args.filename, convert_neg_666=False)
if args.output_filepath is None:
basename = os.path.basename(args.filename)
out_name = os.path.splitext(basename)[0] + ".gctx"
else... | Separate from main() in order to make command-line tool. | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/gct2gctx.py#L48-L76 |
cmap/cmapPy | cmapPy/pandasGEXpress/parse.py | parse | def parse(file_path, convert_neg_666=True, rid=None, cid=None, ridx=None, cidx=None,
row_meta_only=False, col_meta_only=False, make_multiindex=False):
"""
Identifies whether file_path corresponds to a .gct or .gctx file and calls the
correct corresponding parse method.
Input:
Mandator... | python | def parse(file_path, convert_neg_666=True, rid=None, cid=None, ridx=None, cidx=None,
row_meta_only=False, col_meta_only=False, make_multiindex=False):
"""
Identifies whether file_path corresponds to a .gct or .gctx file and calls the
correct corresponding parse method.
Input:
Mandator... | Identifies whether file_path corresponds to a .gct or .gctx file and calls the
correct corresponding parse method.
Input:
Mandatory:
- gct(x)_file_path (str): full path to gct(x) file you want to parse.
Optional:
- convert_neg_666 (bool): whether to convert -666 values to numpy... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/parse.py#L21-L75 |
cmap/cmapPy | cmapPy/math/agg_wt_avg.py | get_upper_triangle | def get_upper_triangle(correlation_matrix):
''' Extract upper triangle from a square matrix. Negative values are
set to 0.
Args:
correlation_matrix (pandas df): Correlations between all replicates
Returns:
upper_tri_df (pandas df): Upper triangle extracted from
correlation_matrix; rid ... | python | def get_upper_triangle(correlation_matrix):
''' Extract upper triangle from a square matrix. Negative values are
set to 0.
Args:
correlation_matrix (pandas df): Correlations between all replicates
Returns:
upper_tri_df (pandas df): Upper triangle extracted from
correlation_matrix; rid ... | Extract upper triangle from a square matrix. Negative values are
set to 0.
Args:
correlation_matrix (pandas df): Correlations between all replicates
Returns:
upper_tri_df (pandas df): Upper triangle extracted from
correlation_matrix; rid is the row index, cid is the column index,
c... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/math/agg_wt_avg.py#L17-L41 |
cmap/cmapPy | cmapPy/math/agg_wt_avg.py | calculate_weights | def calculate_weights(correlation_matrix, min_wt):
''' Calculate a weight for each profile based on its correlation to other
replicates. Negative correlations are clipped to 0, and weights are clipped
to be min_wt at the least.
Args:
correlation_matrix (pandas df): Correlations between all replicat... | python | def calculate_weights(correlation_matrix, min_wt):
''' Calculate a weight for each profile based on its correlation to other
replicates. Negative correlations are clipped to 0, and weights are clipped
to be min_wt at the least.
Args:
correlation_matrix (pandas df): Correlations between all replicat... | Calculate a weight for each profile based on its correlation to other
replicates. Negative correlations are clipped to 0, and weights are clipped
to be min_wt at the least.
Args:
correlation_matrix (pandas df): Correlations between all replicates
min_wt (float): Minimum raw weight when calculating ... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/math/agg_wt_avg.py#L44-L72 |
cmap/cmapPy | cmapPy/math/agg_wt_avg.py | agg_wt_avg | def agg_wt_avg(mat, min_wt = 0.01, corr_metric='spearman'):
''' Aggregate a set of replicate profiles into a single signature using
a weighted average.
Args:
mat (pandas df): a matrix of replicate profiles, where the columns are
samples and the rows are features; columns correspond to the
... | python | def agg_wt_avg(mat, min_wt = 0.01, corr_metric='spearman'):
''' Aggregate a set of replicate profiles into a single signature using
a weighted average.
Args:
mat (pandas df): a matrix of replicate profiles, where the columns are
samples and the rows are features; columns correspond to the
... | Aggregate a set of replicate profiles into a single signature using
a weighted average.
Args:
mat (pandas df): a matrix of replicate profiles, where the columns are
samples and the rows are features; columns correspond to the
replicates of a single perturbagen
min_wt (float): Minimum ra... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/math/agg_wt_avg.py#L75-L118 |
cmap/cmapPy | cmapPy/pandasGEXpress/concat.py | concat_main | def concat_main(args):
""" Separate method from main() in order to make testing easier and to
enable command-line access. """
# Get files directly
if args.input_filepaths is not None:
files = args.input_filepaths
# Or find them
else:
files = get_file_list(args.file_wildcard)
... | python | def concat_main(args):
""" Separate method from main() in order to make testing easier and to
enable command-line access. """
# Get files directly
if args.input_filepaths is not None:
files = args.input_filepaths
# Or find them
else:
files = get_file_list(args.file_wildcard)
... | Separate method from main() in order to make testing easier and to
enable command-line access. | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/concat.py#L106-L155 |
cmap/cmapPy | cmapPy/pandasGEXpress/concat.py | get_file_list | def get_file_list(wildcard):
""" Search for files to be concatenated. Currently very basic, but could
expand to be more sophisticated.
Args:
wildcard (regular expression string)
Returns:
files (list of full file paths)
"""
files = glob.glob(os.path.expanduser(wildcard))
re... | python | def get_file_list(wildcard):
""" Search for files to be concatenated. Currently very basic, but could
expand to be more sophisticated.
Args:
wildcard (regular expression string)
Returns:
files (list of full file paths)
"""
files = glob.glob(os.path.expanduser(wildcard))
re... | Search for files to be concatenated. Currently very basic, but could
expand to be more sophisticated.
Args:
wildcard (regular expression string)
Returns:
files (list of full file paths) | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/concat.py#L158-L170 |
cmap/cmapPy | cmapPy/pandasGEXpress/concat.py | hstack | def hstack(gctoos, remove_all_metadata_fields=False, error_report_file=None, fields_to_remove=[], reset_ids=False):
""" Horizontally concatenate gctoos.
Args:
gctoos (list of gctoo objects)
remove_all_metadata_fields (bool): ignore/strip all common metadata when combining gctoos
error_... | python | def hstack(gctoos, remove_all_metadata_fields=False, error_report_file=None, fields_to_remove=[], reset_ids=False):
""" Horizontally concatenate gctoos.
Args:
gctoos (list of gctoo objects)
remove_all_metadata_fields (bool): ignore/strip all common metadata when combining gctoos
error_... | Horizontally concatenate gctoos.
Args:
gctoos (list of gctoo objects)
remove_all_metadata_fields (bool): ignore/strip all common metadata when combining gctoos
error_report_file (string): path to write file containing error report indicating
problems that occurred during hsta... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/concat.py#L173-L224 |
cmap/cmapPy | cmapPy/pandasGEXpress/concat.py | assemble_common_meta | def assemble_common_meta(common_meta_dfs, fields_to_remove, sources, remove_all_metadata_fields, error_report_file):
""" Assemble the common metadata dfs together. Both indices are sorted.
Fields that are not in all the dfs are dropped.
Args:
common_meta_dfs (list of pandas dfs)
fields_to_r... | python | def assemble_common_meta(common_meta_dfs, fields_to_remove, sources, remove_all_metadata_fields, error_report_file):
""" Assemble the common metadata dfs together. Both indices are sorted.
Fields that are not in all the dfs are dropped.
Args:
common_meta_dfs (list of pandas dfs)
fields_to_r... | Assemble the common metadata dfs together. Both indices are sorted.
Fields that are not in all the dfs are dropped.
Args:
common_meta_dfs (list of pandas dfs)
fields_to_remove (list of strings): fields to be removed from the
common metadata because they don't agree across files
... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/concat.py#L279-L312 |
cmap/cmapPy | cmapPy/pandasGEXpress/concat.py | build_common_all_meta_df | def build_common_all_meta_df(common_meta_dfs, fields_to_remove, remove_all_metadata_fields):
"""
concatenate the entries in common_meta_dfs, removing columns selectively (fields_to_remove) or entirely (
remove_all_metadata_fields=True; in this case, effectively just merges all the indexes in common_meta... | python | def build_common_all_meta_df(common_meta_dfs, fields_to_remove, remove_all_metadata_fields):
"""
concatenate the entries in common_meta_dfs, removing columns selectively (fields_to_remove) or entirely (
remove_all_metadata_fields=True; in this case, effectively just merges all the indexes in common_meta... | concatenate the entries in common_meta_dfs, removing columns selectively (fields_to_remove) or entirely (
remove_all_metadata_fields=True; in this case, effectively just merges all the indexes in common_meta_dfs).
Returns 2 dataframes (in a tuple): the first has duplicates removed, the second does not... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/concat.py#L315-L367 |
cmap/cmapPy | cmapPy/pandasGEXpress/concat.py | build_mismatched_common_meta_report | def build_mismatched_common_meta_report(common_meta_df_shapes, sources, all_meta_df, all_meta_df_with_dups):
"""
Generate a report (dataframe) that indicates for the common metadata that does not match across the common metadata
which source file had which of the different mismatch values
Args:
... | python | def build_mismatched_common_meta_report(common_meta_df_shapes, sources, all_meta_df, all_meta_df_with_dups):
"""
Generate a report (dataframe) that indicates for the common metadata that does not match across the common metadata
which source file had which of the different mismatch values
Args:
... | Generate a report (dataframe) that indicates for the common metadata that does not match across the common metadata
which source file had which of the different mismatch values
Args:
common_meta_df_shapes: list of tuples that are the shapes of the common meta dataframes
sources: list of th... | https://github.com/cmap/cmapPy/blob/59d833b64fd2c3a494cdf67fe1eb11fc8008bf76/cmapPy/pandasGEXpress/concat.py#L370-L420 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.