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19.8k
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12,000
|
datascopeanalytics/scrubadub
|
scrubadub/scrubbers.py
|
Scrubber.clean
|
def clean(self, text, **kwargs):
"""This is the master method that cleans all of the filth out of the
dirty dirty ``text``. All keyword arguments to this function are passed
through to the ``Filth.replace_with`` method to fine-tune how the
``Filth`` is cleaned.
"""
if sys.version_info < (3, 0):
# Only in Python 2. In 3 every string is a Python 2 unicode
if not isinstance(text, unicode):
raise exceptions.UnicodeRequired
clean_chunks = []
filth = Filth()
for next_filth in self.iter_filth(text):
clean_chunks.append(text[filth.end:next_filth.beg])
clean_chunks.append(next_filth.replace_with(**kwargs))
filth = next_filth
clean_chunks.append(text[filth.end:])
return u''.join(clean_chunks)
|
python
|
def clean(self, text, **kwargs):
"""This is the master method that cleans all of the filth out of the
dirty dirty ``text``. All keyword arguments to this function are passed
through to the ``Filth.replace_with`` method to fine-tune how the
``Filth`` is cleaned.
"""
if sys.version_info < (3, 0):
# Only in Python 2. In 3 every string is a Python 2 unicode
if not isinstance(text, unicode):
raise exceptions.UnicodeRequired
clean_chunks = []
filth = Filth()
for next_filth in self.iter_filth(text):
clean_chunks.append(text[filth.end:next_filth.beg])
clean_chunks.append(next_filth.replace_with(**kwargs))
filth = next_filth
clean_chunks.append(text[filth.end:])
return u''.join(clean_chunks)
|
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"]",
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"return",
"u''",
".",
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"(",
"clean_chunks",
")"
] |
This is the master method that cleans all of the filth out of the
dirty dirty ``text``. All keyword arguments to this function are passed
through to the ``Filth.replace_with`` method to fine-tune how the
``Filth`` is cleaned.
|
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"-",
"tune",
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"the",
"Filth",
"is",
"cleaned",
"."
] |
914bda49a16130b44af43df6a2f84755477c407c
|
https://github.com/datascopeanalytics/scrubadub/blob/914bda49a16130b44af43df6a2f84755477c407c/scrubadub/scrubbers.py#L44-L62
|
12,001
|
datascopeanalytics/scrubadub
|
scrubadub/scrubbers.py
|
Scrubber.iter_filth
|
def iter_filth(self, text):
"""Iterate over the different types of filth that can exist.
"""
# currently doing this by aggregating all_filths and then sorting
# inline instead of with a Filth.__cmp__ method, which is apparently
# much slower http://stackoverflow.com/a/988728/564709
#
# NOTE: we could probably do this in a more efficient way by iterating
# over all detectors simultaneously. just trying to get something
# working right now and we can worry about efficiency later
all_filths = []
for detector in self._detectors.values():
for filth in detector.iter_filth(text):
if not isinstance(filth, Filth):
raise TypeError('iter_filth must always yield Filth')
all_filths.append(filth)
# Sort by start position. If two filths start in the same place then
# return the longer one first
all_filths.sort(key=lambda f: (f.beg, -f.end))
# this is where the Scrubber does its hard work and merges any
# overlapping filths.
if not all_filths:
raise StopIteration
filth = all_filths[0]
for next_filth in all_filths[1:]:
if filth.end < next_filth.beg:
yield filth
filth = next_filth
else:
filth = filth.merge(next_filth)
yield filth
|
python
|
def iter_filth(self, text):
"""Iterate over the different types of filth that can exist.
"""
# currently doing this by aggregating all_filths and then sorting
# inline instead of with a Filth.__cmp__ method, which is apparently
# much slower http://stackoverflow.com/a/988728/564709
#
# NOTE: we could probably do this in a more efficient way by iterating
# over all detectors simultaneously. just trying to get something
# working right now and we can worry about efficiency later
all_filths = []
for detector in self._detectors.values():
for filth in detector.iter_filth(text):
if not isinstance(filth, Filth):
raise TypeError('iter_filth must always yield Filth')
all_filths.append(filth)
# Sort by start position. If two filths start in the same place then
# return the longer one first
all_filths.sort(key=lambda f: (f.beg, -f.end))
# this is where the Scrubber does its hard work and merges any
# overlapping filths.
if not all_filths:
raise StopIteration
filth = all_filths[0]
for next_filth in all_filths[1:]:
if filth.end < next_filth.beg:
yield filth
filth = next_filth
else:
filth = filth.merge(next_filth)
yield filth
|
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Iterate over the different types of filth that can exist.
|
[
"Iterate",
"over",
"the",
"different",
"types",
"of",
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"that",
"can",
"exist",
"."
] |
914bda49a16130b44af43df6a2f84755477c407c
|
https://github.com/datascopeanalytics/scrubadub/blob/914bda49a16130b44af43df6a2f84755477c407c/scrubadub/scrubbers.py#L64-L96
|
12,002
|
terrycain/aioboto3
|
aioboto3/s3/inject.py
|
download_file
|
async def download_file(self, Bucket, Key, Filename, ExtraArgs=None, Callback=None, Config=None):
"""Download an S3 object to a file.
Usage::
import boto3
s3 = boto3.resource('s3')
s3.meta.client.download_file('mybucket', 'hello.txt', '/tmp/hello.txt')
Similar behavior as S3Transfer's download_file() method,
except that parameters are capitalized.
"""
with open(Filename, 'wb') as open_file:
await download_fileobj(self, Bucket, Key, open_file, ExtraArgs=ExtraArgs, Callback=Callback, Config=Config)
|
python
|
async def download_file(self, Bucket, Key, Filename, ExtraArgs=None, Callback=None, Config=None):
"""Download an S3 object to a file.
Usage::
import boto3
s3 = boto3.resource('s3')
s3.meta.client.download_file('mybucket', 'hello.txt', '/tmp/hello.txt')
Similar behavior as S3Transfer's download_file() method,
except that parameters are capitalized.
"""
with open(Filename, 'wb') as open_file:
await download_fileobj(self, Bucket, Key, open_file, ExtraArgs=ExtraArgs, Callback=Callback, Config=Config)
|
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",",
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",",
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",",
"Filename",
",",
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",",
"Callback",
"=",
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",",
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")"
] |
Download an S3 object to a file.
Usage::
import boto3
s3 = boto3.resource('s3')
s3.meta.client.download_file('mybucket', 'hello.txt', '/tmp/hello.txt')
Similar behavior as S3Transfer's download_file() method,
except that parameters are capitalized.
|
[
"Download",
"an",
"S3",
"object",
"to",
"a",
"file",
"."
] |
0fd192175461f7bb192f3ed9a872591caf8474ac
|
https://github.com/terrycain/aioboto3/blob/0fd192175461f7bb192f3ed9a872591caf8474ac/aioboto3/s3/inject.py#L17-L30
|
12,003
|
terrycain/aioboto3
|
aioboto3/s3/inject.py
|
download_fileobj
|
async def download_fileobj(self, Bucket, Key, Fileobj, ExtraArgs=None, Callback=None, Config=None):
"""Download an object from S3 to a file-like object.
The file-like object must be in binary mode.
This is a managed transfer which will perform a multipart download in
multiple threads if necessary.
Usage::
import boto3
s3 = boto3.client('s3')
with open('filename', 'wb') as data:
s3.download_fileobj('mybucket', 'mykey', data)
:type Fileobj: a file-like object
:param Fileobj: A file-like object to download into. At a minimum, it must
implement the `write` method and must accept bytes.
:type Bucket: str
:param Bucket: The name of the bucket to download from.
:type Key: str
:param Key: The name of the key to download from.
:type ExtraArgs: dict
:param ExtraArgs: Extra arguments that may be passed to the
client operation.
:type Callback: method
:param Callback: A method which takes a number of bytes transferred to
be periodically called during the download.
:type Config: boto3.s3.transfer.TransferConfig
:param Config: The transfer configuration to be used when performing the
download.
"""
try:
resp = await self.get_object(Bucket=Bucket, Key=Key)
except ClientError as err:
if err.response['Error']['Code'] == 'NoSuchKey':
# Convert to 404 so it looks the same when boto3.download_file fails
raise ClientError({'Error': {'Code': '404', 'Message': 'Not Found'}}, 'HeadObject')
raise
body = resp['Body']
while True:
data = await body.read(4096)
if data == b'':
break
if Callback:
try:
Callback(len(data))
except: # noqa: E722
pass
Fileobj.write(data)
await asyncio.sleep(0.0)
|
python
|
async def download_fileobj(self, Bucket, Key, Fileobj, ExtraArgs=None, Callback=None, Config=None):
"""Download an object from S3 to a file-like object.
The file-like object must be in binary mode.
This is a managed transfer which will perform a multipart download in
multiple threads if necessary.
Usage::
import boto3
s3 = boto3.client('s3')
with open('filename', 'wb') as data:
s3.download_fileobj('mybucket', 'mykey', data)
:type Fileobj: a file-like object
:param Fileobj: A file-like object to download into. At a minimum, it must
implement the `write` method and must accept bytes.
:type Bucket: str
:param Bucket: The name of the bucket to download from.
:type Key: str
:param Key: The name of the key to download from.
:type ExtraArgs: dict
:param ExtraArgs: Extra arguments that may be passed to the
client operation.
:type Callback: method
:param Callback: A method which takes a number of bytes transferred to
be periodically called during the download.
:type Config: boto3.s3.transfer.TransferConfig
:param Config: The transfer configuration to be used when performing the
download.
"""
try:
resp = await self.get_object(Bucket=Bucket, Key=Key)
except ClientError as err:
if err.response['Error']['Code'] == 'NoSuchKey':
# Convert to 404 so it looks the same when boto3.download_file fails
raise ClientError({'Error': {'Code': '404', 'Message': 'Not Found'}}, 'HeadObject')
raise
body = resp['Body']
while True:
data = await body.read(4096)
if data == b'':
break
if Callback:
try:
Callback(len(data))
except: # noqa: E722
pass
Fileobj.write(data)
await asyncio.sleep(0.0)
|
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Download an object from S3 to a file-like object.
The file-like object must be in binary mode.
This is a managed transfer which will perform a multipart download in
multiple threads if necessary.
Usage::
import boto3
s3 = boto3.client('s3')
with open('filename', 'wb') as data:
s3.download_fileobj('mybucket', 'mykey', data)
:type Fileobj: a file-like object
:param Fileobj: A file-like object to download into. At a minimum, it must
implement the `write` method and must accept bytes.
:type Bucket: str
:param Bucket: The name of the bucket to download from.
:type Key: str
:param Key: The name of the key to download from.
:type ExtraArgs: dict
:param ExtraArgs: Extra arguments that may be passed to the
client operation.
:type Callback: method
:param Callback: A method which takes a number of bytes transferred to
be periodically called during the download.
:type Config: boto3.s3.transfer.TransferConfig
:param Config: The transfer configuration to be used when performing the
download.
|
[
"Download",
"an",
"object",
"from",
"S3",
"to",
"a",
"file",
"-",
"like",
"object",
"."
] |
0fd192175461f7bb192f3ed9a872591caf8474ac
|
https://github.com/terrycain/aioboto3/blob/0fd192175461f7bb192f3ed9a872591caf8474ac/aioboto3/s3/inject.py#L33-L95
|
12,004
|
terrycain/aioboto3
|
aioboto3/s3/inject.py
|
upload_fileobj
|
async def upload_fileobj(self, Fileobj: BinaryIO, Bucket: str, Key: str, ExtraArgs: Optional[Dict[str, Any]] = None,
Callback: Optional[Callable[[int], None]] = None,
Config: Optional[S3TransferConfig] = None):
"""Upload a file-like object to S3.
The file-like object must be in binary mode.
This is a managed transfer which will perform a multipart upload in
multiple threads if necessary.
Usage::
import boto3
s3 = boto3.client('s3')
with open('filename', 'rb') as data:
s3.upload_fileobj(data, 'mybucket', 'mykey')
:type Fileobj: a file-like object
:param Fileobj: A file-like object to upload. At a minimum, it must
implement the `read` method, and must return bytes.
:type Bucket: str
:param Bucket: The name of the bucket to upload to.
:type Key: str
:param Key: The name of the key to upload to.
:type ExtraArgs: dict
:param ExtraArgs: Extra arguments that may be passed to the
client operation.
:type Callback: method
:param Callback: A method which takes a number of bytes transferred to
be periodically called during the upload.
:type Config: boto3.s3.transfer.TransferConfig
:param Config: The transfer configuration to be used when performing the
upload.
"""
if not ExtraArgs:
ExtraArgs = {}
# I was debating setting up a queue etc...
# If its too slow I'll then be bothered
multipart_chunksize = 8388608 if Config is None else Config.multipart_chunksize
io_chunksize = 262144 if Config is None else Config.io_chunksize
# max_concurrency = 10 if Config is None else Config.max_concurrency
# max_io_queue = 100 if config is None else Config.max_io_queue
# Start multipart upload
resp = await self.create_multipart_upload(Bucket=Bucket, Key=Key, **ExtraArgs)
upload_id = resp['UploadId']
part = 0
parts = []
running = True
sent_bytes = 0
try:
while running:
part += 1
multipart_payload = b''
while len(multipart_payload) < multipart_chunksize:
if asyncio.iscoroutinefunction(Fileobj.read): # handles if we pass in aiofiles obj
data = await Fileobj.read(io_chunksize)
else:
data = Fileobj.read(io_chunksize)
if data == b'': # End of file
running = False
break
multipart_payload += data
# Submit part to S3
resp = await self.upload_part(
Body=multipart_payload,
Bucket=Bucket,
Key=Key,
PartNumber=part,
UploadId=upload_id
)
parts.append({'ETag': resp['ETag'], 'PartNumber': part})
sent_bytes += len(multipart_payload)
try:
Callback(sent_bytes) # Attempt to call the callback, if it fails, ignore, if no callback, ignore
except: # noqa: E722
pass
# By now the uploads must have been done
await self.complete_multipart_upload(
Bucket=Bucket,
Key=Key,
UploadId=upload_id,
MultipartUpload={'Parts': parts}
)
except: # noqa: E722
# Cancel multipart upload
await self.abort_multipart_upload(
Bucket=Bucket,
Key=Key,
UploadId=upload_id
)
raise
|
python
|
async def upload_fileobj(self, Fileobj: BinaryIO, Bucket: str, Key: str, ExtraArgs: Optional[Dict[str, Any]] = None,
Callback: Optional[Callable[[int], None]] = None,
Config: Optional[S3TransferConfig] = None):
"""Upload a file-like object to S3.
The file-like object must be in binary mode.
This is a managed transfer which will perform a multipart upload in
multiple threads if necessary.
Usage::
import boto3
s3 = boto3.client('s3')
with open('filename', 'rb') as data:
s3.upload_fileobj(data, 'mybucket', 'mykey')
:type Fileobj: a file-like object
:param Fileobj: A file-like object to upload. At a minimum, it must
implement the `read` method, and must return bytes.
:type Bucket: str
:param Bucket: The name of the bucket to upload to.
:type Key: str
:param Key: The name of the key to upload to.
:type ExtraArgs: dict
:param ExtraArgs: Extra arguments that may be passed to the
client operation.
:type Callback: method
:param Callback: A method which takes a number of bytes transferred to
be periodically called during the upload.
:type Config: boto3.s3.transfer.TransferConfig
:param Config: The transfer configuration to be used when performing the
upload.
"""
if not ExtraArgs:
ExtraArgs = {}
# I was debating setting up a queue etc...
# If its too slow I'll then be bothered
multipart_chunksize = 8388608 if Config is None else Config.multipart_chunksize
io_chunksize = 262144 if Config is None else Config.io_chunksize
# max_concurrency = 10 if Config is None else Config.max_concurrency
# max_io_queue = 100 if config is None else Config.max_io_queue
# Start multipart upload
resp = await self.create_multipart_upload(Bucket=Bucket, Key=Key, **ExtraArgs)
upload_id = resp['UploadId']
part = 0
parts = []
running = True
sent_bytes = 0
try:
while running:
part += 1
multipart_payload = b''
while len(multipart_payload) < multipart_chunksize:
if asyncio.iscoroutinefunction(Fileobj.read): # handles if we pass in aiofiles obj
data = await Fileobj.read(io_chunksize)
else:
data = Fileobj.read(io_chunksize)
if data == b'': # End of file
running = False
break
multipart_payload += data
# Submit part to S3
resp = await self.upload_part(
Body=multipart_payload,
Bucket=Bucket,
Key=Key,
PartNumber=part,
UploadId=upload_id
)
parts.append({'ETag': resp['ETag'], 'PartNumber': part})
sent_bytes += len(multipart_payload)
try:
Callback(sent_bytes) # Attempt to call the callback, if it fails, ignore, if no callback, ignore
except: # noqa: E722
pass
# By now the uploads must have been done
await self.complete_multipart_upload(
Bucket=Bucket,
Key=Key,
UploadId=upload_id,
MultipartUpload={'Parts': parts}
)
except: # noqa: E722
# Cancel multipart upload
await self.abort_multipart_upload(
Bucket=Bucket,
Key=Key,
UploadId=upload_id
)
raise
|
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"async",
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"=",
"Bucket",
",",
"Key",
"=",
"Key",
",",
"UploadId",
"=",
"upload_id",
")",
"raise"
] |
Upload a file-like object to S3.
The file-like object must be in binary mode.
This is a managed transfer which will perform a multipart upload in
multiple threads if necessary.
Usage::
import boto3
s3 = boto3.client('s3')
with open('filename', 'rb') as data:
s3.upload_fileobj(data, 'mybucket', 'mykey')
:type Fileobj: a file-like object
:param Fileobj: A file-like object to upload. At a minimum, it must
implement the `read` method, and must return bytes.
:type Bucket: str
:param Bucket: The name of the bucket to upload to.
:type Key: str
:param Key: The name of the key to upload to.
:type ExtraArgs: dict
:param ExtraArgs: Extra arguments that may be passed to the
client operation.
:type Callback: method
:param Callback: A method which takes a number of bytes transferred to
be periodically called during the upload.
:type Config: boto3.s3.transfer.TransferConfig
:param Config: The transfer configuration to be used when performing the
upload.
|
[
"Upload",
"a",
"file",
"-",
"like",
"object",
"to",
"S3",
"."
] |
0fd192175461f7bb192f3ed9a872591caf8474ac
|
https://github.com/terrycain/aioboto3/blob/0fd192175461f7bb192f3ed9a872591caf8474ac/aioboto3/s3/inject.py#L98-L203
|
12,005
|
terrycain/aioboto3
|
aioboto3/s3/inject.py
|
upload_file
|
async def upload_file(self, Filename, Bucket, Key, ExtraArgs=None, Callback=None, Config=None):
"""Upload a file to an S3 object.
Usage::
import boto3
s3 = boto3.resource('s3')
s3.meta.client.upload_file('/tmp/hello.txt', 'mybucket', 'hello.txt')
Similar behavior as S3Transfer's upload_file() method,
except that parameters are capitalized.
"""
with open(Filename, 'rb') as open_file:
await upload_fileobj(self, open_file, Bucket, Key, ExtraArgs=ExtraArgs, Callback=Callback, Config=Config)
|
python
|
async def upload_file(self, Filename, Bucket, Key, ExtraArgs=None, Callback=None, Config=None):
"""Upload a file to an S3 object.
Usage::
import boto3
s3 = boto3.resource('s3')
s3.meta.client.upload_file('/tmp/hello.txt', 'mybucket', 'hello.txt')
Similar behavior as S3Transfer's upload_file() method,
except that parameters are capitalized.
"""
with open(Filename, 'rb') as open_file:
await upload_fileobj(self, open_file, Bucket, Key, ExtraArgs=ExtraArgs, Callback=Callback, Config=Config)
|
[
"async",
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",",
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",",
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"ExtraArgs",
"=",
"ExtraArgs",
",",
"Callback",
"=",
"Callback",
",",
"Config",
"=",
"Config",
")"
] |
Upload a file to an S3 object.
Usage::
import boto3
s3 = boto3.resource('s3')
s3.meta.client.upload_file('/tmp/hello.txt', 'mybucket', 'hello.txt')
Similar behavior as S3Transfer's upload_file() method,
except that parameters are capitalized.
|
[
"Upload",
"a",
"file",
"to",
"an",
"S3",
"object",
"."
] |
0fd192175461f7bb192f3ed9a872591caf8474ac
|
https://github.com/terrycain/aioboto3/blob/0fd192175461f7bb192f3ed9a872591caf8474ac/aioboto3/s3/inject.py#L206-L219
|
12,006
|
terrycain/aioboto3
|
aioboto3/resources.py
|
AIOBoto3ResourceFactory._create_action
|
def _create_action(factory_self, action_model, resource_name,
service_context, is_load=False):
"""
Creates a new method which makes a request to the underlying
AWS service.
"""
# Create the action in in this closure but before the ``do_action``
# method below is invoked, which allows instances of the resource
# to share the ServiceAction instance.
action = AIOServiceAction(
action_model, factory=factory_self,
service_context=service_context
)
# A resource's ``load`` method is special because it sets
# values on the resource instead of returning the response.
if is_load:
# We need a new method here because we want access to the
# instance via ``self``.
async def do_action(self, *args, **kwargs):
# response = action(self, *args, **kwargs)
response = await action.async_call(self, *args, **kwargs)
self.meta.data = response
# Create the docstring for the load/reload mehtods.
lazy_docstring = docstring.LoadReloadDocstring(
action_name=action_model.name,
resource_name=resource_name,
event_emitter=factory_self._emitter,
load_model=action_model,
service_model=service_context.service_model,
include_signature=False
)
else:
# We need a new method here because we want access to the
# instance via ``self``.
async def do_action(self, *args, **kwargs):
response = await action.async_call(self, *args, **kwargs)
if hasattr(self, 'load'):
# Clear cached data. It will be reloaded the next
# time that an attribute is accessed.
# TODO: Make this configurable in the future?
self.meta.data = None
return response
lazy_docstring = docstring.ActionDocstring(
resource_name=resource_name,
event_emitter=factory_self._emitter,
action_model=action_model,
service_model=service_context.service_model,
include_signature=False
)
do_action.__name__ = str(action_model.name)
do_action.__doc__ = lazy_docstring
return do_action
|
python
|
def _create_action(factory_self, action_model, resource_name,
service_context, is_load=False):
"""
Creates a new method which makes a request to the underlying
AWS service.
"""
# Create the action in in this closure but before the ``do_action``
# method below is invoked, which allows instances of the resource
# to share the ServiceAction instance.
action = AIOServiceAction(
action_model, factory=factory_self,
service_context=service_context
)
# A resource's ``load`` method is special because it sets
# values on the resource instead of returning the response.
if is_load:
# We need a new method here because we want access to the
# instance via ``self``.
async def do_action(self, *args, **kwargs):
# response = action(self, *args, **kwargs)
response = await action.async_call(self, *args, **kwargs)
self.meta.data = response
# Create the docstring for the load/reload mehtods.
lazy_docstring = docstring.LoadReloadDocstring(
action_name=action_model.name,
resource_name=resource_name,
event_emitter=factory_self._emitter,
load_model=action_model,
service_model=service_context.service_model,
include_signature=False
)
else:
# We need a new method here because we want access to the
# instance via ``self``.
async def do_action(self, *args, **kwargs):
response = await action.async_call(self, *args, **kwargs)
if hasattr(self, 'load'):
# Clear cached data. It will be reloaded the next
# time that an attribute is accessed.
# TODO: Make this configurable in the future?
self.meta.data = None
return response
lazy_docstring = docstring.ActionDocstring(
resource_name=resource_name,
event_emitter=factory_self._emitter,
action_model=action_model,
service_model=service_context.service_model,
include_signature=False
)
do_action.__name__ = str(action_model.name)
do_action.__doc__ = lazy_docstring
return do_action
|
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] |
Creates a new method which makes a request to the underlying
AWS service.
|
[
"Creates",
"a",
"new",
"method",
"which",
"makes",
"a",
"request",
"to",
"the",
"underlying",
"AWS",
"service",
"."
] |
0fd192175461f7bb192f3ed9a872591caf8474ac
|
https://github.com/terrycain/aioboto3/blob/0fd192175461f7bb192f3ed9a872591caf8474ac/aioboto3/resources.py#L183-L240
|
12,007
|
terrycain/aioboto3
|
aioboto3/s3/cse.py
|
AsymmetricCryptoContext.from_der_private_key
|
def from_der_private_key(data: bytes, password: Optional[str] = None) -> _RSAPrivateKey:
"""
Convert private key in DER encoding to a Private key object
:param data: private key bytes
:param password: password the private key is encrypted with
"""
return serialization.load_der_private_key(data, password, default_backend())
|
python
|
def from_der_private_key(data: bytes, password: Optional[str] = None) -> _RSAPrivateKey:
"""
Convert private key in DER encoding to a Private key object
:param data: private key bytes
:param password: password the private key is encrypted with
"""
return serialization.load_der_private_key(data, password, default_backend())
|
[
"def",
"from_der_private_key",
"(",
"data",
":",
"bytes",
",",
"password",
":",
"Optional",
"[",
"str",
"]",
"=",
"None",
")",
"->",
"_RSAPrivateKey",
":",
"return",
"serialization",
".",
"load_der_private_key",
"(",
"data",
",",
"password",
",",
"default_backend",
"(",
")",
")"
] |
Convert private key in DER encoding to a Private key object
:param data: private key bytes
:param password: password the private key is encrypted with
|
[
"Convert",
"private",
"key",
"in",
"DER",
"encoding",
"to",
"a",
"Private",
"key",
"object"
] |
0fd192175461f7bb192f3ed9a872591caf8474ac
|
https://github.com/terrycain/aioboto3/blob/0fd192175461f7bb192f3ed9a872591caf8474ac/aioboto3/s3/cse.py#L149-L156
|
12,008
|
terrycain/aioboto3
|
aioboto3/s3/cse.py
|
S3CSE.get_object
|
async def get_object(self, Bucket: str, Key: str, **kwargs) -> dict:
"""
S3 GetObject. Takes same args as Boto3 documentation
Decrypts any CSE
:param Bucket: S3 Bucket
:param Key: S3 Key (filepath)
:return: returns same response as a normal S3 get_object
"""
if self._s3_client is None:
await self.setup()
# Ok so if we are doing a range get. We need to align the range start/end with AES block boundaries
# 9223372036854775806 is 8EiB so I have no issue with hardcoding it.
# We pass the actual start, desired start and desired end to the decrypt function so that it can
# generate the correct IV's for starting decryption at that block and then chop off the start and end of the
# AES block so it matches what the user is expecting.
_range = kwargs.get('Range')
actual_range_start = None
desired_range_start = None
desired_range_end = None
if _range:
range_match = RANGE_REGEX.match(_range)
if not range_match:
raise ValueError('Dont understand this range value {0}'.format(_range))
desired_range_start = int(range_match.group(1))
desired_range_end = range_match.group(2)
if desired_range_end is None:
desired_range_end = 9223372036854775806
else:
desired_range_end = int(desired_range_end)
actual_range_start, actual_range_end = _get_adjusted_crypto_range(desired_range_start, desired_range_end)
# Update range with actual start_end
kwargs['Range'] = 'bytes={0}-{1}'.format(actual_range_start, actual_range_end)
s3_response = await self._s3_client.get_object(Bucket=Bucket, Key=Key, **kwargs)
file_data = await s3_response['Body'].read()
metadata = s3_response['Metadata']
whole_file_length = int(s3_response['ResponseMetadata']['HTTPHeaders']['content-length'])
if 'x-amz-key' not in metadata and 'x-amz-key-v2' not in metadata:
# No crypto
return s3_response
if 'x-amz-key' in metadata:
# Crypto V1
body = await self._decrypt_v1(file_data, metadata, actual_range_start)
else:
# Crypto V2
body = await self._decrypt_v2(file_data, metadata, whole_file_length,
actual_range_start, desired_range_start,
desired_range_end)
s3_response['Body'] = DummyAIOFile(body)
return s3_response
|
python
|
async def get_object(self, Bucket: str, Key: str, **kwargs) -> dict:
"""
S3 GetObject. Takes same args as Boto3 documentation
Decrypts any CSE
:param Bucket: S3 Bucket
:param Key: S3 Key (filepath)
:return: returns same response as a normal S3 get_object
"""
if self._s3_client is None:
await self.setup()
# Ok so if we are doing a range get. We need to align the range start/end with AES block boundaries
# 9223372036854775806 is 8EiB so I have no issue with hardcoding it.
# We pass the actual start, desired start and desired end to the decrypt function so that it can
# generate the correct IV's for starting decryption at that block and then chop off the start and end of the
# AES block so it matches what the user is expecting.
_range = kwargs.get('Range')
actual_range_start = None
desired_range_start = None
desired_range_end = None
if _range:
range_match = RANGE_REGEX.match(_range)
if not range_match:
raise ValueError('Dont understand this range value {0}'.format(_range))
desired_range_start = int(range_match.group(1))
desired_range_end = range_match.group(2)
if desired_range_end is None:
desired_range_end = 9223372036854775806
else:
desired_range_end = int(desired_range_end)
actual_range_start, actual_range_end = _get_adjusted_crypto_range(desired_range_start, desired_range_end)
# Update range with actual start_end
kwargs['Range'] = 'bytes={0}-{1}'.format(actual_range_start, actual_range_end)
s3_response = await self._s3_client.get_object(Bucket=Bucket, Key=Key, **kwargs)
file_data = await s3_response['Body'].read()
metadata = s3_response['Metadata']
whole_file_length = int(s3_response['ResponseMetadata']['HTTPHeaders']['content-length'])
if 'x-amz-key' not in metadata and 'x-amz-key-v2' not in metadata:
# No crypto
return s3_response
if 'x-amz-key' in metadata:
# Crypto V1
body = await self._decrypt_v1(file_data, metadata, actual_range_start)
else:
# Crypto V2
body = await self._decrypt_v2(file_data, metadata, whole_file_length,
actual_range_start, desired_range_start,
desired_range_end)
s3_response['Body'] = DummyAIOFile(body)
return s3_response
|
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"]",
"=",
"DummyAIOFile",
"(",
"body",
")",
"return",
"s3_response"
] |
S3 GetObject. Takes same args as Boto3 documentation
Decrypts any CSE
:param Bucket: S3 Bucket
:param Key: S3 Key (filepath)
:return: returns same response as a normal S3 get_object
|
[
"S3",
"GetObject",
".",
"Takes",
"same",
"args",
"as",
"Boto3",
"documentation"
] |
0fd192175461f7bb192f3ed9a872591caf8474ac
|
https://github.com/terrycain/aioboto3/blob/0fd192175461f7bb192f3ed9a872591caf8474ac/aioboto3/s3/cse.py#L330-L389
|
12,009
|
terrycain/aioboto3
|
aioboto3/s3/cse.py
|
S3CSE.put_object
|
async def put_object(self, Body: Union[bytes, IO], Bucket: str, Key: str, Metadata: Dict = None, **kwargs):
"""
PutObject. Takes same args as Boto3 documentation
Encrypts files
:param: Body: File data
:param Bucket: S3 Bucket
:param Key: S3 Key (filepath)
"""
if self._s3_client is None:
await self.setup()
if hasattr(Body, 'read'):
if inspect.iscoroutinefunction(Body.read):
Body = await Body.read()
else:
Body = Body.read()
# We do some different V2 stuff if using kms
is_kms = isinstance(self._crypto_context, KMSCryptoContext)
# noinspection PyUnresolvedReferences
authenticated_crypto = is_kms and self._crypto_context.authenticated_encryption
Metadata = Metadata if Metadata is not None else {}
aes_key, matdesc_metadata, key_metadata = await self._crypto_context.get_encryption_aes_key()
if is_kms and authenticated_crypto:
Metadata['x-amz-cek-alg'] = 'AES/GCM/NoPadding'
Metadata['x-amz-tag-len'] = str(AES_BLOCK_SIZE)
iv = os.urandom(12)
# 16byte 128bit authentication tag forced
aesgcm = AESGCM(aes_key)
result = await self._loop.run_in_executor(None, lambda: aesgcm.encrypt(iv, Body, None))
else:
if is_kms: # V1 is always AES/CBC/PKCS5Padding
Metadata['x-amz-cek-alg'] = 'AES/CBC/PKCS5Padding'
iv = os.urandom(16)
padder = PKCS7(AES.block_size).padder()
padded_result = await self._loop.run_in_executor(None, lambda: (padder.update(Body) + padder.finalize()))
aescbc = Cipher(AES(aes_key), CBC(iv), backend=self._backend).encryptor()
result = await self._loop.run_in_executor(None, lambda: (aescbc.update(padded_result) + aescbc.finalize()))
# For all V1 and V2
Metadata['x-amz-unencrypted-content-length'] = str(len(Body))
Metadata['x-amz-iv'] = base64.b64encode(iv).decode()
Metadata['x-amz-matdesc'] = json.dumps(matdesc_metadata)
if is_kms:
Metadata['x-amz-wrap-alg'] = 'kms'
Metadata['x-amz-key-v2'] = key_metadata
else:
Metadata['x-amz-key'] = key_metadata
await self._s3_client.put_object(
Bucket=Bucket,
Key=Key,
Body=result,
Metadata=Metadata,
**kwargs
)
|
python
|
async def put_object(self, Body: Union[bytes, IO], Bucket: str, Key: str, Metadata: Dict = None, **kwargs):
"""
PutObject. Takes same args as Boto3 documentation
Encrypts files
:param: Body: File data
:param Bucket: S3 Bucket
:param Key: S3 Key (filepath)
"""
if self._s3_client is None:
await self.setup()
if hasattr(Body, 'read'):
if inspect.iscoroutinefunction(Body.read):
Body = await Body.read()
else:
Body = Body.read()
# We do some different V2 stuff if using kms
is_kms = isinstance(self._crypto_context, KMSCryptoContext)
# noinspection PyUnresolvedReferences
authenticated_crypto = is_kms and self._crypto_context.authenticated_encryption
Metadata = Metadata if Metadata is not None else {}
aes_key, matdesc_metadata, key_metadata = await self._crypto_context.get_encryption_aes_key()
if is_kms and authenticated_crypto:
Metadata['x-amz-cek-alg'] = 'AES/GCM/NoPadding'
Metadata['x-amz-tag-len'] = str(AES_BLOCK_SIZE)
iv = os.urandom(12)
# 16byte 128bit authentication tag forced
aesgcm = AESGCM(aes_key)
result = await self._loop.run_in_executor(None, lambda: aesgcm.encrypt(iv, Body, None))
else:
if is_kms: # V1 is always AES/CBC/PKCS5Padding
Metadata['x-amz-cek-alg'] = 'AES/CBC/PKCS5Padding'
iv = os.urandom(16)
padder = PKCS7(AES.block_size).padder()
padded_result = await self._loop.run_in_executor(None, lambda: (padder.update(Body) + padder.finalize()))
aescbc = Cipher(AES(aes_key), CBC(iv), backend=self._backend).encryptor()
result = await self._loop.run_in_executor(None, lambda: (aescbc.update(padded_result) + aescbc.finalize()))
# For all V1 and V2
Metadata['x-amz-unencrypted-content-length'] = str(len(Body))
Metadata['x-amz-iv'] = base64.b64encode(iv).decode()
Metadata['x-amz-matdesc'] = json.dumps(matdesc_metadata)
if is_kms:
Metadata['x-amz-wrap-alg'] = 'kms'
Metadata['x-amz-key-v2'] = key_metadata
else:
Metadata['x-amz-key'] = key_metadata
await self._s3_client.put_object(
Bucket=Bucket,
Key=Key,
Body=result,
Metadata=Metadata,
**kwargs
)
|
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PutObject. Takes same args as Boto3 documentation
Encrypts files
:param: Body: File data
:param Bucket: S3 Bucket
:param Key: S3 Key (filepath)
|
[
"PutObject",
".",
"Takes",
"same",
"args",
"as",
"Boto3",
"documentation"
] |
0fd192175461f7bb192f3ed9a872591caf8474ac
|
https://github.com/terrycain/aioboto3/blob/0fd192175461f7bb192f3ed9a872591caf8474ac/aioboto3/s3/cse.py#L482-L549
|
12,010
|
astrofrog/fast-histogram
|
fast_histogram/histogram.py
|
histogram1d
|
def histogram1d(x, bins, range, weights=None):
"""
Compute a 1D histogram assuming equally spaced bins.
Parameters
----------
x : `~numpy.ndarray`
The position of the points to bin in the 1D histogram
bins : int
The number of bins
range : iterable
The range as a tuple of (xmin, xmax)
weights : `~numpy.ndarray`
The weights of the points in the 1D histogram
Returns
-------
array : `~numpy.ndarray`
The 1D histogram array
"""
nx = bins
if not np.isscalar(bins):
raise TypeError('bins should be an integer')
xmin, xmax = range
if not np.isfinite(xmin):
raise ValueError("xmin should be finite")
if not np.isfinite(xmax):
raise ValueError("xmax should be finite")
if xmax <= xmin:
raise ValueError("xmax should be greater than xmin")
if nx <= 0:
raise ValueError("nx should be strictly positive")
if weights is None:
return _histogram1d(x, nx, xmin, xmax)
else:
return _histogram1d_weighted(x, weights, nx, xmin, xmax)
|
python
|
def histogram1d(x, bins, range, weights=None):
"""
Compute a 1D histogram assuming equally spaced bins.
Parameters
----------
x : `~numpy.ndarray`
The position of the points to bin in the 1D histogram
bins : int
The number of bins
range : iterable
The range as a tuple of (xmin, xmax)
weights : `~numpy.ndarray`
The weights of the points in the 1D histogram
Returns
-------
array : `~numpy.ndarray`
The 1D histogram array
"""
nx = bins
if not np.isscalar(bins):
raise TypeError('bins should be an integer')
xmin, xmax = range
if not np.isfinite(xmin):
raise ValueError("xmin should be finite")
if not np.isfinite(xmax):
raise ValueError("xmax should be finite")
if xmax <= xmin:
raise ValueError("xmax should be greater than xmin")
if nx <= 0:
raise ValueError("nx should be strictly positive")
if weights is None:
return _histogram1d(x, nx, xmin, xmax)
else:
return _histogram1d_weighted(x, weights, nx, xmin, xmax)
|
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Compute a 1D histogram assuming equally spaced bins.
Parameters
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The position of the points to bin in the 1D histogram
bins : int
The number of bins
range : iterable
The range as a tuple of (xmin, xmax)
weights : `~numpy.ndarray`
The weights of the points in the 1D histogram
Returns
-------
array : `~numpy.ndarray`
The 1D histogram array
|
[
"Compute",
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"1D",
"histogram",
"assuming",
"equally",
"spaced",
"bins",
"."
] |
ace4f2444fba2e21fa3cd9dad966f6b65b60660f
|
https://github.com/astrofrog/fast-histogram/blob/ace4f2444fba2e21fa3cd9dad966f6b65b60660f/fast_histogram/histogram.py#L15-L58
|
12,011
|
astrofrog/fast-histogram
|
fast_histogram/histogram.py
|
histogram2d
|
def histogram2d(x, y, bins, range, weights=None):
"""
Compute a 2D histogram assuming equally spaced bins.
Parameters
----------
x, y : `~numpy.ndarray`
The position of the points to bin in the 2D histogram
bins : int or iterable
The number of bins in each dimension. If given as an integer, the same
number of bins is used for each dimension.
range : iterable
The range to use in each dimention, as an iterable of value pairs, i.e.
[(xmin, xmax), (ymin, ymax)]
weights : `~numpy.ndarray`
The weights of the points in the 1D histogram
Returns
-------
array : `~numpy.ndarray`
The 2D histogram array
"""
if isinstance(bins, numbers.Integral):
nx = ny = bins
else:
nx, ny = bins
if not np.isscalar(nx) or not np.isscalar(ny):
raise TypeError('bins should be an iterable of two integers')
(xmin, xmax), (ymin, ymax) = range
if not np.isfinite(xmin):
raise ValueError("xmin should be finite")
if not np.isfinite(xmax):
raise ValueError("xmax should be finite")
if not np.isfinite(ymin):
raise ValueError("ymin should be finite")
if not np.isfinite(ymax):
raise ValueError("ymax should be finite")
if xmax <= xmin:
raise ValueError("xmax should be greater than xmin")
if ymax <= ymin:
raise ValueError("xmax should be greater than xmin")
if nx <= 0:
raise ValueError("nx should be strictly positive")
if ny <= 0:
raise ValueError("ny should be strictly positive")
if weights is None:
return _histogram2d(x, y, nx, xmin, xmax, ny, ymin, ymax)
else:
return _histogram2d_weighted(x, y, weights, nx, xmin, xmax, ny, ymin, ymax)
|
python
|
def histogram2d(x, y, bins, range, weights=None):
"""
Compute a 2D histogram assuming equally spaced bins.
Parameters
----------
x, y : `~numpy.ndarray`
The position of the points to bin in the 2D histogram
bins : int or iterable
The number of bins in each dimension. If given as an integer, the same
number of bins is used for each dimension.
range : iterable
The range to use in each dimention, as an iterable of value pairs, i.e.
[(xmin, xmax), (ymin, ymax)]
weights : `~numpy.ndarray`
The weights of the points in the 1D histogram
Returns
-------
array : `~numpy.ndarray`
The 2D histogram array
"""
if isinstance(bins, numbers.Integral):
nx = ny = bins
else:
nx, ny = bins
if not np.isscalar(nx) or not np.isscalar(ny):
raise TypeError('bins should be an iterable of two integers')
(xmin, xmax), (ymin, ymax) = range
if not np.isfinite(xmin):
raise ValueError("xmin should be finite")
if not np.isfinite(xmax):
raise ValueError("xmax should be finite")
if not np.isfinite(ymin):
raise ValueError("ymin should be finite")
if not np.isfinite(ymax):
raise ValueError("ymax should be finite")
if xmax <= xmin:
raise ValueError("xmax should be greater than xmin")
if ymax <= ymin:
raise ValueError("xmax should be greater than xmin")
if nx <= 0:
raise ValueError("nx should be strictly positive")
if ny <= 0:
raise ValueError("ny should be strictly positive")
if weights is None:
return _histogram2d(x, y, nx, xmin, xmax, ny, ymin, ymax)
else:
return _histogram2d_weighted(x, y, weights, nx, xmin, xmax, ny, ymin, ymax)
|
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",",
"weights",
",",
"nx",
",",
"xmin",
",",
"xmax",
",",
"ny",
",",
"ymin",
",",
"ymax",
")"
] |
Compute a 2D histogram assuming equally spaced bins.
Parameters
----------
x, y : `~numpy.ndarray`
The position of the points to bin in the 2D histogram
bins : int or iterable
The number of bins in each dimension. If given as an integer, the same
number of bins is used for each dimension.
range : iterable
The range to use in each dimention, as an iterable of value pairs, i.e.
[(xmin, xmax), (ymin, ymax)]
weights : `~numpy.ndarray`
The weights of the points in the 1D histogram
Returns
-------
array : `~numpy.ndarray`
The 2D histogram array
|
[
"Compute",
"a",
"2D",
"histogram",
"assuming",
"equally",
"spaced",
"bins",
"."
] |
ace4f2444fba2e21fa3cd9dad966f6b65b60660f
|
https://github.com/astrofrog/fast-histogram/blob/ace4f2444fba2e21fa3cd9dad966f6b65b60660f/fast_histogram/histogram.py#L61-L121
|
12,012
|
cytoscape/py2cytoscape
|
py2cytoscape/data/cynetwork.py
|
CyNetwork.to_networkx
|
def to_networkx(self):
"""
Return this network in NetworkX graph object.
:return: Network as NetworkX graph object
"""
return nx_util.to_networkx(self.session.get(self.__url).json())
|
python
|
def to_networkx(self):
"""
Return this network in NetworkX graph object.
:return: Network as NetworkX graph object
"""
return nx_util.to_networkx(self.session.get(self.__url).json())
|
[
"def",
"to_networkx",
"(",
"self",
")",
":",
"return",
"nx_util",
".",
"to_networkx",
"(",
"self",
".",
"session",
".",
"get",
"(",
"self",
".",
"__url",
")",
".",
"json",
"(",
")",
")"
] |
Return this network in NetworkX graph object.
:return: Network as NetworkX graph object
|
[
"Return",
"this",
"network",
"in",
"NetworkX",
"graph",
"object",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/cynetwork.py#L46-L52
|
12,013
|
cytoscape/py2cytoscape
|
py2cytoscape/data/cynetwork.py
|
CyNetwork.to_dataframe
|
def to_dataframe(self, extra_edges_columns=[]):
"""
Return this network in pandas DataFrame.
:return: Network as DataFrame. This is equivalent to SIF.
"""
return df_util.to_dataframe(
self.session.get(self.__url).json(),
edges_attr_cols=extra_edges_columns
)
|
python
|
def to_dataframe(self, extra_edges_columns=[]):
"""
Return this network in pandas DataFrame.
:return: Network as DataFrame. This is equivalent to SIF.
"""
return df_util.to_dataframe(
self.session.get(self.__url).json(),
edges_attr_cols=extra_edges_columns
)
|
[
"def",
"to_dataframe",
"(",
"self",
",",
"extra_edges_columns",
"=",
"[",
"]",
")",
":",
"return",
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".",
"to_dataframe",
"(",
"self",
".",
"session",
".",
"get",
"(",
"self",
".",
"__url",
")",
".",
"json",
"(",
")",
",",
"edges_attr_cols",
"=",
"extra_edges_columns",
")"
] |
Return this network in pandas DataFrame.
:return: Network as DataFrame. This is equivalent to SIF.
|
[
"Return",
"this",
"network",
"in",
"pandas",
"DataFrame",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/cynetwork.py#L54-L63
|
12,014
|
cytoscape/py2cytoscape
|
py2cytoscape/data/cynetwork.py
|
CyNetwork.add_node
|
def add_node(self, node_name, dataframe=False):
""" Add a single node to the network. """
if node_name is None:
return None
return self.add_nodes([node_name], dataframe=dataframe)
|
python
|
def add_node(self, node_name, dataframe=False):
""" Add a single node to the network. """
if node_name is None:
return None
return self.add_nodes([node_name], dataframe=dataframe)
|
[
"def",
"add_node",
"(",
"self",
",",
"node_name",
",",
"dataframe",
"=",
"False",
")",
":",
"if",
"node_name",
"is",
"None",
":",
"return",
"None",
"return",
"self",
".",
"add_nodes",
"(",
"[",
"node_name",
"]",
",",
"dataframe",
"=",
"dataframe",
")"
] |
Add a single node to the network.
|
[
"Add",
"a",
"single",
"node",
"to",
"the",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/cynetwork.py#L82-L86
|
12,015
|
cytoscape/py2cytoscape
|
py2cytoscape/data/cynetwork.py
|
CyNetwork.add_nodes
|
def add_nodes(self, node_name_list, dataframe=False):
"""
Add new nodes to the network
:param node_name_list: list of node names, e.g. ['a', 'b', 'c']
:param dataframe: If True, return a pandas dataframe instead of a dict.
:return: A dict mapping names to SUIDs for the newly-created nodes.
"""
res = self.session.post(self.__url + 'nodes', data=json.dumps(node_name_list), headers=HEADERS)
check_response(res)
nodes = res.json()
if dataframe:
return pd.DataFrame(nodes).set_index(['SUID'])
else:
return {node['name']: node['SUID'] for node in nodes}
|
python
|
def add_nodes(self, node_name_list, dataframe=False):
"""
Add new nodes to the network
:param node_name_list: list of node names, e.g. ['a', 'b', 'c']
:param dataframe: If True, return a pandas dataframe instead of a dict.
:return: A dict mapping names to SUIDs for the newly-created nodes.
"""
res = self.session.post(self.__url + 'nodes', data=json.dumps(node_name_list), headers=HEADERS)
check_response(res)
nodes = res.json()
if dataframe:
return pd.DataFrame(nodes).set_index(['SUID'])
else:
return {node['name']: node['SUID'] for node in nodes}
|
[
"def",
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",",
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"[",
"'name'",
"]",
":",
"node",
"[",
"'SUID'",
"]",
"for",
"node",
"in",
"nodes",
"}"
] |
Add new nodes to the network
:param node_name_list: list of node names, e.g. ['a', 'b', 'c']
:param dataframe: If True, return a pandas dataframe instead of a dict.
:return: A dict mapping names to SUIDs for the newly-created nodes.
|
[
"Add",
"new",
"nodes",
"to",
"the",
"network"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/cynetwork.py#L88-L102
|
12,016
|
cytoscape/py2cytoscape
|
py2cytoscape/data/cynetwork.py
|
CyNetwork.add_edge
|
def add_edge(self, source, target, interaction='-', directed=True, dataframe=True):
""" Add a single edge from source to target. """
new_edge = {
'source': source,
'target': target,
'interaction': interaction,
'directed': directed
}
return self.add_edges([new_edge], dataframe=dataframe)
|
python
|
def add_edge(self, source, target, interaction='-', directed=True, dataframe=True):
""" Add a single edge from source to target. """
new_edge = {
'source': source,
'target': target,
'interaction': interaction,
'directed': directed
}
return self.add_edges([new_edge], dataframe=dataframe)
|
[
"def",
"add_edge",
"(",
"self",
",",
"source",
",",
"target",
",",
"interaction",
"=",
"'-'",
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"directed",
"=",
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",",
"dataframe",
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"self",
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"add_edges",
"(",
"[",
"new_edge",
"]",
",",
"dataframe",
"=",
"dataframe",
")"
] |
Add a single edge from source to target.
|
[
"Add",
"a",
"single",
"edge",
"from",
"source",
"to",
"target",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/cynetwork.py#L104-L112
|
12,017
|
cytoscape/py2cytoscape
|
py2cytoscape/data/cynetwork.py
|
CyNetwork.get_views
|
def get_views(self):
"""
Get views as a list of SUIDs
:return:
"""
url = self.__url + 'views'
return self.session.get(url).json()
|
python
|
def get_views(self):
"""
Get views as a list of SUIDs
:return:
"""
url = self.__url + 'views'
return self.session.get(url).json()
|
[
"def",
"get_views",
"(",
"self",
")",
":",
"url",
"=",
"self",
".",
"__url",
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"'views'",
"return",
"self",
".",
"session",
".",
"get",
"(",
"url",
")",
".",
"json",
"(",
")"
] |
Get views as a list of SUIDs
:return:
|
[
"Get",
"views",
"as",
"a",
"list",
"of",
"SUIDs"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/cynetwork.py#L304-L311
|
12,018
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/diffusion.py
|
diffusion.diffuse_advanced
|
def diffuse_advanced(self, heatColumnName=None, time=None, verbose=False):
"""
Diffusion will send the selected network view and its selected nodes to
a web-based REST service to calculate network propagation. Results are
returned and represented by columns in the node table.
Columns are created for each execution of Diffusion and their names are
returned in the response.
:param heatColumnName (string, optional): A node column name intended
to override the default table column 'diffusion_input'. This represents
the query vector and corresponds to h in the diffusion equation. =
['HEKScore', 'JurkatScore', '(Use selected nodes)']
:param time (string, optional): The extent of spread over the network.
This corresponds to t in the diffusion equation.
:param verbose: print more
"""
PARAMS=set_param(["heatColumnName","time"],[heatColumnName,time])
response=api(url=self.__url+"/diffuse_advanced", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def diffuse_advanced(self, heatColumnName=None, time=None, verbose=False):
"""
Diffusion will send the selected network view and its selected nodes to
a web-based REST service to calculate network propagation. Results are
returned and represented by columns in the node table.
Columns are created for each execution of Diffusion and their names are
returned in the response.
:param heatColumnName (string, optional): A node column name intended
to override the default table column 'diffusion_input'. This represents
the query vector and corresponds to h in the diffusion equation. =
['HEKScore', 'JurkatScore', '(Use selected nodes)']
:param time (string, optional): The extent of spread over the network.
This corresponds to t in the diffusion equation.
:param verbose: print more
"""
PARAMS=set_param(["heatColumnName","time"],[heatColumnName,time])
response=api(url=self.__url+"/diffuse_advanced", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
"def",
"diffuse_advanced",
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"heatColumnName",
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"None",
",",
"time",
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"None",
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"=",
"False",
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"PARAMS",
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"[",
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",",
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"heatColumnName",
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"url",
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"__url",
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"PARAMS",
",",
"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Diffusion will send the selected network view and its selected nodes to
a web-based REST service to calculate network propagation. Results are
returned and represented by columns in the node table.
Columns are created for each execution of Diffusion and their names are
returned in the response.
:param heatColumnName (string, optional): A node column name intended
to override the default table column 'diffusion_input'. This represents
the query vector and corresponds to h in the diffusion equation. =
['HEKScore', 'JurkatScore', '(Use selected nodes)']
:param time (string, optional): The extent of spread over the network.
This corresponds to t in the diffusion equation.
:param verbose: print more
|
[
"Diffusion",
"will",
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"the",
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"and",
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"-",
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"and",
"their",
"names",
"are",
"returned",
"in",
"the",
"response",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/diffusion.py#L30-L48
|
12,019
|
cytoscape/py2cytoscape
|
py2cytoscape/util/util_networkx.py
|
to_networkx
|
def to_networkx(cyjs, directed=True):
"""
Convert Cytoscape.js-style JSON object into NetworkX object.
By default, data will be handles as a directed graph.
"""
if directed:
g = nx.MultiDiGraph()
else:
g = nx.MultiGraph()
network_data = cyjs[DATA]
if network_data is not None:
for key in network_data.keys():
g.graph[key] = network_data[key]
nodes = cyjs[ELEMENTS][NODES]
edges = cyjs[ELEMENTS][EDGES]
for node in nodes:
data = node[DATA]
g.add_node(data[ID], attr_dict=data)
for edge in edges:
data = edge[DATA]
source = data[SOURCE]
target = data[TARGET]
g.add_edge(source, target, attr_dict=data)
return g
|
python
|
def to_networkx(cyjs, directed=True):
"""
Convert Cytoscape.js-style JSON object into NetworkX object.
By default, data will be handles as a directed graph.
"""
if directed:
g = nx.MultiDiGraph()
else:
g = nx.MultiGraph()
network_data = cyjs[DATA]
if network_data is not None:
for key in network_data.keys():
g.graph[key] = network_data[key]
nodes = cyjs[ELEMENTS][NODES]
edges = cyjs[ELEMENTS][EDGES]
for node in nodes:
data = node[DATA]
g.add_node(data[ID], attr_dict=data)
for edge in edges:
data = edge[DATA]
source = data[SOURCE]
target = data[TARGET]
g.add_edge(source, target, attr_dict=data)
return g
|
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"add_edge",
"(",
"source",
",",
"target",
",",
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"=",
"data",
")",
"return",
"g"
] |
Convert Cytoscape.js-style JSON object into NetworkX object.
By default, data will be handles as a directed graph.
|
[
"Convert",
"Cytoscape",
".",
"js",
"-",
"style",
"JSON",
"object",
"into",
"NetworkX",
"object",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/util/util_networkx.py#L120-L151
|
12,020
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/cybrowser.py
|
cybrowser.dialog
|
def dialog(self=None, wid=None, text=None, title=None, url=None, debug=False, verbose=False):
"""
Launch and HTML browser in a separate window.
:param wid: Window ID
:param text: HTML text
:param title: Window Title
:param url: URL
:param debug: Show debug tools. boolean
:param verbose: print more
"""
PARAMS=set_param(["id","text","title","url","debug"],[wid,text,title,url,debug])
response=api(url=self.__url+"/dialog?",PARAMS=PARAMS, method="GET", verbose=verbose)
return response
|
python
|
def dialog(self=None, wid=None, text=None, title=None, url=None, debug=False, verbose=False):
"""
Launch and HTML browser in a separate window.
:param wid: Window ID
:param text: HTML text
:param title: Window Title
:param url: URL
:param debug: Show debug tools. boolean
:param verbose: print more
"""
PARAMS=set_param(["id","text","title","url","debug"],[wid,text,title,url,debug])
response=api(url=self.__url+"/dialog?",PARAMS=PARAMS, method="GET", verbose=verbose)
return response
|
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Launch and HTML browser in a separate window.
:param wid: Window ID
:param text: HTML text
:param title: Window Title
:param url: URL
:param debug: Show debug tools. boolean
:param verbose: print more
|
[
"Launch",
"and",
"HTML",
"browser",
"in",
"a",
"separate",
"window",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/cybrowser.py#L13-L27
|
12,021
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/cybrowser.py
|
cybrowser.hide
|
def hide(self, wid, verbose=False):
"""
Hide and HTML browser in the Results Panel.
:param wid: Window ID
:param verbose: print more
"""
PARAMS={"id":wid}
response=api(url=self.__url+"/hide?",PARAMS=PARAMS, method="GET", verbose=verbose)
return response
|
python
|
def hide(self, wid, verbose=False):
"""
Hide and HTML browser in the Results Panel.
:param wid: Window ID
:param verbose: print more
"""
PARAMS={"id":wid}
response=api(url=self.__url+"/hide?",PARAMS=PARAMS, method="GET", verbose=verbose)
return response
|
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Hide and HTML browser in the Results Panel.
:param wid: Window ID
:param verbose: print more
|
[
"Hide",
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"Panel",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/cybrowser.py#L29-L40
|
12,022
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/cybrowser.py
|
cybrowser.show
|
def show(self, wid=None, text=None, title=None, url=None, verbose=False):
"""
Launch an HTML browser in the Results Panel.
:param wid: Window ID
:param text: HTML text
:param title: Window Title
:param url: URL
:param verbose: print more
"""
PARAMS={}
for p,v in zip(["id","text","title","url"],[wid,text,title,url]):
if v:
PARAMS[p]=v
response=api(url=self.__url+"/show?",PARAMS=PARAMS, method="GET", verbose=verbose)
return response
|
python
|
def show(self, wid=None, text=None, title=None, url=None, verbose=False):
"""
Launch an HTML browser in the Results Panel.
:param wid: Window ID
:param text: HTML text
:param title: Window Title
:param url: URL
:param verbose: print more
"""
PARAMS={}
for p,v in zip(["id","text","title","url"],[wid,text,title,url]):
if v:
PARAMS[p]=v
response=api(url=self.__url+"/show?",PARAMS=PARAMS, method="GET", verbose=verbose)
return response
|
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Launch an HTML browser in the Results Panel.
:param wid: Window ID
:param text: HTML text
:param title: Window Title
:param url: URL
:param verbose: print more
|
[
"Launch",
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"browser",
"in",
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"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/cybrowser.py#L42-L59
|
12,023
|
cytoscape/py2cytoscape
|
py2cytoscape/data/util_http.py
|
check_response
|
def check_response(res):
""" Check HTTP response and raise exception if response is not OK. """
try:
res.raise_for_status() # Alternative is res.ok
except Exception as exc:
# Bad response code, e.g. if adding an edge with nodes that doesn't exist
try:
err_info = res.json()
err_msg = err_info['message'] # or 'localizeMessage'
except ValueError:
err_msg = res.text[:40] # Take the first 40 chars of the response
except KeyError:
err_msg = res.text[:40] + ("(No 'message' in err_info dict: %s"
% list(err_info.keys()))
exc.args += (err_msg,)
raise exc
|
python
|
def check_response(res):
""" Check HTTP response and raise exception if response is not OK. """
try:
res.raise_for_status() # Alternative is res.ok
except Exception as exc:
# Bad response code, e.g. if adding an edge with nodes that doesn't exist
try:
err_info = res.json()
err_msg = err_info['message'] # or 'localizeMessage'
except ValueError:
err_msg = res.text[:40] # Take the first 40 chars of the response
except KeyError:
err_msg = res.text[:40] + ("(No 'message' in err_info dict: %s"
% list(err_info.keys()))
exc.args += (err_msg,)
raise exc
|
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Check HTTP response and raise exception if response is not OK.
|
[
"Check",
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"OK",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/util_http.py#L3-L18
|
12,024
|
cytoscape/py2cytoscape
|
py2cytoscape/util/util_dataframe.py
|
from_dataframe
|
def from_dataframe(df,
source_col='source',
target_col='target',
interaction_col='interaction',
name='From DataFrame',
edge_attr_cols=[]):
"""
Utility to convert Pandas DataFrame object into Cytoscape.js JSON
:param df: Dataframe to convert.
:param source_col: Name of source column.
:param target_col: Name of target column.
:param interaction_col: Name of interaction column.
:param name: Name of network.
:param edge_attr_cols: List containing other columns to consider in df as
edges' attributes.
:return: Dictionary version of df.
"""
network = cyjs.get_empty_network(name=name)
nodes = set()
if edge_attr_cols is None:
edge_attr_cols = []
for index, row in df.iterrows():
s = row[source_col]
t = row[target_col]
if s not in nodes:
nodes.add(s)
source = get_node(s)
network['elements']['nodes'].append(source)
if t not in nodes:
nodes.add(t)
target = get_node(t)
network['elements']['nodes'].append(target)
extra_values = {column: row[column]
for column in edge_attr_cols
if column in df.columns}
network['elements']['edges'].append(
get_edge(s, t, interaction=row[interaction_col], **extra_values)
)
return network
|
python
|
def from_dataframe(df,
source_col='source',
target_col='target',
interaction_col='interaction',
name='From DataFrame',
edge_attr_cols=[]):
"""
Utility to convert Pandas DataFrame object into Cytoscape.js JSON
:param df: Dataframe to convert.
:param source_col: Name of source column.
:param target_col: Name of target column.
:param interaction_col: Name of interaction column.
:param name: Name of network.
:param edge_attr_cols: List containing other columns to consider in df as
edges' attributes.
:return: Dictionary version of df.
"""
network = cyjs.get_empty_network(name=name)
nodes = set()
if edge_attr_cols is None:
edge_attr_cols = []
for index, row in df.iterrows():
s = row[source_col]
t = row[target_col]
if s not in nodes:
nodes.add(s)
source = get_node(s)
network['elements']['nodes'].append(source)
if t not in nodes:
nodes.add(t)
target = get_node(t)
network['elements']['nodes'].append(target)
extra_values = {column: row[column]
for column in edge_attr_cols
if column in df.columns}
network['elements']['edges'].append(
get_edge(s, t, interaction=row[interaction_col], **extra_values)
)
return network
|
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Utility to convert Pandas DataFrame object into Cytoscape.js JSON
:param df: Dataframe to convert.
:param source_col: Name of source column.
:param target_col: Name of target column.
:param interaction_col: Name of interaction column.
:param name: Name of network.
:param edge_attr_cols: List containing other columns to consider in df as
edges' attributes.
:return: Dictionary version of df.
|
[
"Utility",
"to",
"convert",
"Pandas",
"DataFrame",
"object",
"into",
"Cytoscape",
".",
"js",
"JSON"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/util/util_dataframe.py#L6-L49
|
12,025
|
cytoscape/py2cytoscape
|
py2cytoscape/util/util_dataframe.py
|
to_dataframe
|
def to_dataframe(network,
interaction='interaction',
default_interaction='-',
edges_attr_cols=[]):
"""
Utility to convert a Cytoscape dictionary into a Pandas Dataframe.
:param network: Dictionary to convert.
:param interaction: Name of interaction column.
:param default_interaction: Default value for missing interactions.
:param edges_attr_cols: List containing other edges' attributes to include
in the Dataframe, if present in network.
:return: Converted Pandas Dataframe.
"""
edges = network['elements']['edges']
if edges_attr_cols is None:
edges_attr_cols = []
edges_attr_cols = sorted(edges_attr_cols)
network_array = []
# the set avoids duplicates
valid_extra_cols = set()
for edge in edges:
edge_data = edge['data']
source = edge_data['source']
target = edge_data['target']
if interaction in edge_data:
itr = edge_data[interaction]
else:
itr = default_interaction
extra_values = []
for extra_column in edges_attr_cols:
if extra_column in edge_data:
extra_values.append(edge_data[extra_column])
valid_extra_cols.add(extra_column)
row = tuple([source, itr, target] + extra_values)
network_array.append(row)
return pd.DataFrame( network_array, columns=['source', 'interaction', 'target'] + sorted(valid_extra_cols))
|
python
|
def to_dataframe(network,
interaction='interaction',
default_interaction='-',
edges_attr_cols=[]):
"""
Utility to convert a Cytoscape dictionary into a Pandas Dataframe.
:param network: Dictionary to convert.
:param interaction: Name of interaction column.
:param default_interaction: Default value for missing interactions.
:param edges_attr_cols: List containing other edges' attributes to include
in the Dataframe, if present in network.
:return: Converted Pandas Dataframe.
"""
edges = network['elements']['edges']
if edges_attr_cols is None:
edges_attr_cols = []
edges_attr_cols = sorted(edges_attr_cols)
network_array = []
# the set avoids duplicates
valid_extra_cols = set()
for edge in edges:
edge_data = edge['data']
source = edge_data['source']
target = edge_data['target']
if interaction in edge_data:
itr = edge_data[interaction]
else:
itr = default_interaction
extra_values = []
for extra_column in edges_attr_cols:
if extra_column in edge_data:
extra_values.append(edge_data[extra_column])
valid_extra_cols.add(extra_column)
row = tuple([source, itr, target] + extra_values)
network_array.append(row)
return pd.DataFrame( network_array, columns=['source', 'interaction', 'target'] + sorted(valid_extra_cols))
|
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Utility to convert a Cytoscape dictionary into a Pandas Dataframe.
:param network: Dictionary to convert.
:param interaction: Name of interaction column.
:param default_interaction: Default value for missing interactions.
:param edges_attr_cols: List containing other edges' attributes to include
in the Dataframe, if present in network.
:return: Converted Pandas Dataframe.
|
[
"Utility",
"to",
"convert",
"a",
"Cytoscape",
"dictionary",
"into",
"a",
"Pandas",
"Dataframe",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/util/util_dataframe.py#L52-L91
|
12,026
|
cytoscape/py2cytoscape
|
py2cytoscape/cytoscapejs/viewer.py
|
render
|
def render(network,
style=DEF_STYLE,
layout_algorithm=DEF_LAYOUT,
background=DEF_BACKGROUND_COLOR,
height=DEF_HEIGHT,
width=DEF_WIDTH,
style_file=STYLE_FILE,
def_nodes=DEF_NODES,
def_edges=DEF_EDGES):
"""Render network data with embedded Cytoscape.js widget.
:param network: dict (required)
The network data should be in Cytoscape.js JSON format.
:param style: str or dict
If str, pick one of the preset style. [default: 'default']
If dict, it should be Cytoscape.js style CSS object
:param layout_algorithm: str
Name of Cytoscape.js layout algorithm
:param background: str
Background in CSS format
:param height: int
Height of the widget.
:param width: int
Width of the widget.
:param style_file: a styles file. [default: 'default_style.json']
:param def_nodes: default: [
{'data': {'id': 'Network Data'}},
{'data': {'id': 'Empty'}} ]
:param def_edges: default: [ {'data': {'id': 'is', 'source': 'Network Data', 'target': 'Empty'}} ]
"""
from jinja2 import Template
from IPython.core.display import display, HTML
STYLES=set_styles(style_file)
# Load style file if none available
if isinstance(style, str):
# Specified by name
style = STYLES[style]
if network is None:
nodes = def_nodes
edges = def_edges
else:
nodes = network['elements']['nodes']
edges = network['elements']['edges']
path = os.path.abspath(os.path.dirname(__file__)) + '/' + HTML_TEMPLATE_FILE
template = Template(open(path).read())
cyjs_widget = template.render(
nodes=json.dumps(nodes),
edges=json.dumps(edges),
background=background,
uuid="cy" + str(uuid.uuid4()),
widget_width=str(width),
widget_height=str(height),
layout=layout_algorithm,
style_json=json.dumps(style)
)
display(HTML(cyjs_widget))
|
python
|
def render(network,
style=DEF_STYLE,
layout_algorithm=DEF_LAYOUT,
background=DEF_BACKGROUND_COLOR,
height=DEF_HEIGHT,
width=DEF_WIDTH,
style_file=STYLE_FILE,
def_nodes=DEF_NODES,
def_edges=DEF_EDGES):
"""Render network data with embedded Cytoscape.js widget.
:param network: dict (required)
The network data should be in Cytoscape.js JSON format.
:param style: str or dict
If str, pick one of the preset style. [default: 'default']
If dict, it should be Cytoscape.js style CSS object
:param layout_algorithm: str
Name of Cytoscape.js layout algorithm
:param background: str
Background in CSS format
:param height: int
Height of the widget.
:param width: int
Width of the widget.
:param style_file: a styles file. [default: 'default_style.json']
:param def_nodes: default: [
{'data': {'id': 'Network Data'}},
{'data': {'id': 'Empty'}} ]
:param def_edges: default: [ {'data': {'id': 'is', 'source': 'Network Data', 'target': 'Empty'}} ]
"""
from jinja2 import Template
from IPython.core.display import display, HTML
STYLES=set_styles(style_file)
# Load style file if none available
if isinstance(style, str):
# Specified by name
style = STYLES[style]
if network is None:
nodes = def_nodes
edges = def_edges
else:
nodes = network['elements']['nodes']
edges = network['elements']['edges']
path = os.path.abspath(os.path.dirname(__file__)) + '/' + HTML_TEMPLATE_FILE
template = Template(open(path).read())
cyjs_widget = template.render(
nodes=json.dumps(nodes),
edges=json.dumps(edges),
background=background,
uuid="cy" + str(uuid.uuid4()),
widget_width=str(width),
widget_height=str(height),
layout=layout_algorithm,
style_json=json.dumps(style)
)
display(HTML(cyjs_widget))
|
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Render network data with embedded Cytoscape.js widget.
:param network: dict (required)
The network data should be in Cytoscape.js JSON format.
:param style: str or dict
If str, pick one of the preset style. [default: 'default']
If dict, it should be Cytoscape.js style CSS object
:param layout_algorithm: str
Name of Cytoscape.js layout algorithm
:param background: str
Background in CSS format
:param height: int
Height of the widget.
:param width: int
Width of the widget.
:param style_file: a styles file. [default: 'default_style.json']
:param def_nodes: default: [
{'data': {'id': 'Network Data'}},
{'data': {'id': 'Empty'}} ]
:param def_edges: default: [ {'data': {'id': 'is', 'source': 'Network Data', 'target': 'Empty'}} ]
|
[
"Render",
"network",
"data",
"with",
"embedded",
"Cytoscape",
".",
"js",
"widget",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cytoscapejs/viewer.py#L57-L118
|
12,027
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/edge.py
|
edge.create_attribute
|
def create_attribute(self,column=None,listType=None,namespace=None, network=None, atype=None, verbose=False):
"""
Creates a new edge column.
:param column (string, optional): Unique name of column
:param listType (string, optional): Can be one of integer, long, double,
or string.
:param namespace (string, optional): Node, Edge, and Network objects
support the default, local, and hidden namespaces. Root networks
also support the shared namespace. Custom namespaces may be specified
by Apps.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param atype (string, optional): Can be one of integer, long, double,
string, or list.
:param verbose: print more
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["column","listType","namespace","network","type"],[column,listType,namespace,network,atype])
response=api(url=self.__url+"/create attribute", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def create_attribute(self,column=None,listType=None,namespace=None, network=None, atype=None, verbose=False):
"""
Creates a new edge column.
:param column (string, optional): Unique name of column
:param listType (string, optional): Can be one of integer, long, double,
or string.
:param namespace (string, optional): Node, Edge, and Network objects
support the default, local, and hidden namespaces. Root networks
also support the shared namespace. Custom namespaces may be specified
by Apps.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param atype (string, optional): Can be one of integer, long, double,
string, or list.
:param verbose: print more
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["column","listType","namespace","network","type"],[column,listType,namespace,network,atype])
response=api(url=self.__url+"/create attribute", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Creates a new edge column.
:param column (string, optional): Unique name of column
:param listType (string, optional): Can be one of integer, long, double,
or string.
:param namespace (string, optional): Node, Edge, and Network objects
support the default, local, and hidden namespaces. Root networks
also support the shared namespace. Custom namespaces may be specified
by Apps.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param atype (string, optional): Can be one of integer, long, double,
string, or list.
:param verbose: print more
|
[
"Creates",
"a",
"new",
"edge",
"column",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/edge.py#L13-L35
|
12,028
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/edge.py
|
edge.get
|
def get(self,edge=None,network=None,sourceNode=None, targetNode=None, atype=None, verbose=False):
"""
Returns the SUID of an edge that matches the passed parameters. If
multiple edges are found, only one will be returned, and a warning will
be reported in the Cytoscape Task History dialog.
:param edge (string, optional): Selects an edge by name, or, if the
parameter has the prefix suid:, selects an edge by SUID. If this
parameter is set, all other edge matching parameters are ignored.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param sourceNode (string, optional): Selects a node by name, or, if
the parameter has the prefix suid:, selects a node by SUID. Specifies
that the edge matched must have this node as its source. This parameter
must be used with the targetNode parameter to produce results.
:param targetNode (string, optional): Selects a node by name, or, if
the parameter has the prefix suid:, selects a node by SUID. Specifies
that the edge matched must have this node as its target. This parameter
must be used with the sourceNode parameter to produce results.
:param atype (string, optional): Specifies that the edge matched must
be of the specified type. This parameter must be used with the
sourceNode and targetNode parameters to produce results.
:param verbose: print more
:returns: {"columnName": columnName }
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["edge","network","sourceNode","targetNode","type"],[edge,network,sourceNode,targetNode,atype])
response=api(url=self.__url+"/get", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def get(self,edge=None,network=None,sourceNode=None, targetNode=None, atype=None, verbose=False):
"""
Returns the SUID of an edge that matches the passed parameters. If
multiple edges are found, only one will be returned, and a warning will
be reported in the Cytoscape Task History dialog.
:param edge (string, optional): Selects an edge by name, or, if the
parameter has the prefix suid:, selects an edge by SUID. If this
parameter is set, all other edge matching parameters are ignored.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param sourceNode (string, optional): Selects a node by name, or, if
the parameter has the prefix suid:, selects a node by SUID. Specifies
that the edge matched must have this node as its source. This parameter
must be used with the targetNode parameter to produce results.
:param targetNode (string, optional): Selects a node by name, or, if
the parameter has the prefix suid:, selects a node by SUID. Specifies
that the edge matched must have this node as its target. This parameter
must be used with the sourceNode parameter to produce results.
:param atype (string, optional): Specifies that the edge matched must
be of the specified type. This parameter must be used with the
sourceNode and targetNode parameters to produce results.
:param verbose: print more
:returns: {"columnName": columnName }
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["edge","network","sourceNode","targetNode","type"],[edge,network,sourceNode,targetNode,atype])
response=api(url=self.__url+"/get", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Returns the SUID of an edge that matches the passed parameters. If
multiple edges are found, only one will be returned, and a warning will
be reported in the Cytoscape Task History dialog.
:param edge (string, optional): Selects an edge by name, or, if the
parameter has the prefix suid:, selects an edge by SUID. If this
parameter is set, all other edge matching parameters are ignored.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param sourceNode (string, optional): Selects a node by name, or, if
the parameter has the prefix suid:, selects a node by SUID. Specifies
that the edge matched must have this node as its source. This parameter
must be used with the targetNode parameter to produce results.
:param targetNode (string, optional): Selects a node by name, or, if
the parameter has the prefix suid:, selects a node by SUID. Specifies
that the edge matched must have this node as its target. This parameter
must be used with the sourceNode parameter to produce results.
:param atype (string, optional): Specifies that the edge matched must
be of the specified type. This parameter must be used with the
sourceNode and targetNode parameters to produce results.
:param verbose: print more
:returns: {"columnName": columnName }
|
[
"Returns",
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] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/edge.py#L37-L68
|
12,029
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/network.py
|
network.add_edge
|
def add_edge(self, isDirected=None,name=None,network=None,sourceName=None,targetName=None, verbose=False):
"""
Add a new edge between two existing nodes in a network. The names of the
nodes must be specified and much match the value in the 'name' column for
each node.
:param isDirected (string, optional): Whether the edge should be directed
or not. Even though all edges in Cytoscape have a source and target, by
default they are treated as undirected. Setting this to 'true' will
flag some algorithms to treat them as directed, although many current
implementations will ignore this flag.
:param name (string, optional): Set the 'name' and 'shared name' columns
for this edge to the provided value. ,
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value can
also be used to specify the current network.
:param sourceName (string): Enter the name of an existing node in the
network to be the source of the edge. Note that this is the name as
defined in the 'name' column of the network.
:param targetName (string): Enter the name of an existing node in the
network to be the target of the edge. Note that this is the name as
defined in the 'name' column of the network.
:param verbose: print more
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["isDirected","name","network","sourceName","targetName"],\
[isDirected,name,network,sourceName,targetName])
response=api(url=self.__url+"/add edge", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def add_edge(self, isDirected=None,name=None,network=None,sourceName=None,targetName=None, verbose=False):
"""
Add a new edge between two existing nodes in a network. The names of the
nodes must be specified and much match the value in the 'name' column for
each node.
:param isDirected (string, optional): Whether the edge should be directed
or not. Even though all edges in Cytoscape have a source and target, by
default they are treated as undirected. Setting this to 'true' will
flag some algorithms to treat them as directed, although many current
implementations will ignore this flag.
:param name (string, optional): Set the 'name' and 'shared name' columns
for this edge to the provided value. ,
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value can
also be used to specify the current network.
:param sourceName (string): Enter the name of an existing node in the
network to be the source of the edge. Note that this is the name as
defined in the 'name' column of the network.
:param targetName (string): Enter the name of an existing node in the
network to be the target of the edge. Note that this is the name as
defined in the 'name' column of the network.
:param verbose: print more
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["isDirected","name","network","sourceName","targetName"],\
[isDirected,name,network,sourceName,targetName])
response=api(url=self.__url+"/add edge", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Add a new edge between two existing nodes in a network. The names of the
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each node.
:param isDirected (string, optional): Whether the edge should be directed
or not. Even though all edges in Cytoscape have a source and target, by
default they are treated as undirected. Setting this to 'true' will
flag some algorithms to treat them as directed, although many current
implementations will ignore this flag.
:param name (string, optional): Set the 'name' and 'shared name' columns
for this edge to the provided value. ,
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value can
also be used to specify the current network.
:param sourceName (string): Enter the name of an existing node in the
network to be the source of the edge. Note that this is the name as
defined in the 'name' column of the network.
:param targetName (string): Enter the name of an existing node in the
network to be the target of the edge. Note that this is the name as
defined in the 'name' column of the network.
:param verbose: print more
|
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] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/network.py#L45-L73
|
12,030
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/network.py
|
network.create
|
def create(self, edgeList=None, excludeEdges=None, networkName=None, nodeList=None, source=None, verbose=False):
"""
Create a new network from a list of nodes and edges in an existing source network.
The SUID of the network and view are returned.
:param edgeList (string, optional): Specifies a list of edges. The keywords
all, selected, or unselected can be used to specify edges by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix is
not used, the NAME column is matched by default. A list of COLUMN:VALUE
pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to
match multiple values.
:param excludeEdges (string, optional): Unless this is set to true, edges
that connect nodes in the nodeList are implicitly included
:param networkName (string, optional):
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix is
not used, the NAME column is matched by default. A list of COLUMN:VALUE
pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to
match multiple values.
:param source (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value can
also be used to specify the current network.
:param verbose: print more
:returns: { netowrk, view }
"""
network=check_network(self,source, verbose=verbose)
PARAMS=set_param(["edgeList","excludeEdges","networkName","nodeList","source"], \
[edgeList,excludeEdges,networkName,nodeList,network])
response=api(url=self.__url+"/create", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def create(self, edgeList=None, excludeEdges=None, networkName=None, nodeList=None, source=None, verbose=False):
"""
Create a new network from a list of nodes and edges in an existing source network.
The SUID of the network and view are returned.
:param edgeList (string, optional): Specifies a list of edges. The keywords
all, selected, or unselected can be used to specify edges by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix is
not used, the NAME column is matched by default. A list of COLUMN:VALUE
pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to
match multiple values.
:param excludeEdges (string, optional): Unless this is set to true, edges
that connect nodes in the nodeList are implicitly included
:param networkName (string, optional):
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix is
not used, the NAME column is matched by default. A list of COLUMN:VALUE
pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to
match multiple values.
:param source (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value can
also be used to specify the current network.
:param verbose: print more
:returns: { netowrk, view }
"""
network=check_network(self,source, verbose=verbose)
PARAMS=set_param(["edgeList","excludeEdges","networkName","nodeList","source"], \
[edgeList,excludeEdges,networkName,nodeList,network])
response=api(url=self.__url+"/create", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Create a new network from a list of nodes and edges in an existing source network.
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:param edgeList (string, optional): Specifies a list of edges. The keywords
all, selected, or unselected can be used to specify edges by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix is
not used, the NAME column is matched by default. A list of COLUMN:VALUE
pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to
match multiple values.
:param excludeEdges (string, optional): Unless this is set to true, edges
that connect nodes in the nodeList are implicitly included
:param networkName (string, optional):
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix is
not used, the NAME column is matched by default. A list of COLUMN:VALUE
pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to
match multiple values.
:param source (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value can
also be used to specify the current network.
:param verbose: print more
:returns: { netowrk, view }
|
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"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/network.py#L137-L170
|
12,031
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/network.py
|
network.create_empty
|
def create_empty(self, name=None, renderers=None, RootNetworkList=None, verbose=False):
"""
Create a new, empty network. The new network may be created as part of
an existing network collection or a new network collection.
:param name (string, optional): Enter the name of the new network.
:param renderers (string, optional): Select the renderer to use for the
new network view. By default, the standard Cytoscape 2D renderer (Ding)
will be used = [''],
:param RootNetworkList (string, optional): Choose the network collection
the new network should be part of. If no network collection is selected,
a new network collection is created. = [' -- Create new network collection --',
'cy:command_documentation_generation']
:param verbose: print more
"""
PARAMS=set_param(["name","renderers","RootNetworkList"],[name,renderers,RootNetworkList])
response=api(url=self.__url+"/create empty", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def create_empty(self, name=None, renderers=None, RootNetworkList=None, verbose=False):
"""
Create a new, empty network. The new network may be created as part of
an existing network collection or a new network collection.
:param name (string, optional): Enter the name of the new network.
:param renderers (string, optional): Select the renderer to use for the
new network view. By default, the standard Cytoscape 2D renderer (Ding)
will be used = [''],
:param RootNetworkList (string, optional): Choose the network collection
the new network should be part of. If no network collection is selected,
a new network collection is created. = [' -- Create new network collection --',
'cy:command_documentation_generation']
:param verbose: print more
"""
PARAMS=set_param(["name","renderers","RootNetworkList"],[name,renderers,RootNetworkList])
response=api(url=self.__url+"/create empty", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Create a new, empty network. The new network may be created as part of
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:param name (string, optional): Enter the name of the new network.
:param renderers (string, optional): Select the renderer to use for the
new network view. By default, the standard Cytoscape 2D renderer (Ding)
will be used = [''],
:param RootNetworkList (string, optional): Choose the network collection
the new network should be part of. If no network collection is selected,
a new network collection is created. = [' -- Create new network collection --',
'cy:command_documentation_generation']
:param verbose: print more
|
[
"Create",
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"an",
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"collection",
"or",
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"new",
"network",
"collection",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/network.py#L201-L218
|
12,032
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/network.py
|
network.list
|
def list(self, verbose=False):
"""
List all of the networks in the current session.
:param verbose: print more
:returns: [ list of network suids ]
"""
response=api(url=self.__url+"/list", method="POST", verbose=verbose)
return response
|
python
|
def list(self, verbose=False):
"""
List all of the networks in the current session.
:param verbose: print more
:returns: [ list of network suids ]
"""
response=api(url=self.__url+"/list", method="POST", verbose=verbose)
return response
|
[
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] |
List all of the networks in the current session.
:param verbose: print more
:returns: [ list of network suids ]
|
[
"List",
"all",
"of",
"the",
"networks",
"in",
"the",
"current",
"session",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/network.py#L532-L542
|
12,033
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/network.py
|
network.list_attributes
|
def list_attributes(self, namespace=None, network=None, verbose=False):
"""
Returns a list of column names assocated with a network.
:param namespace (string, optional): Node, Edge, and Network objects
support the default, local, and hidden namespaces. Root networks also
support the shared namespace. Custom namespaces may be specified
by Apps.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param verbose: print more
:returns: [ list of column names assocated with a network ]
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["namespace","network"],[namespace,network])
response=api(url=self.__url+"/list attributes", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def list_attributes(self, namespace=None, network=None, verbose=False):
"""
Returns a list of column names assocated with a network.
:param namespace (string, optional): Node, Edge, and Network objects
support the default, local, and hidden namespaces. Root networks also
support the shared namespace. Custom namespaces may be specified
by Apps.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param verbose: print more
:returns: [ list of column names assocated with a network ]
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["namespace","network"],[namespace,network])
response=api(url=self.__url+"/list attributes", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Returns a list of column names assocated with a network.
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support the default, local, and hidden namespaces. Root networks also
support the shared namespace. Custom namespaces may be specified
by Apps.
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param verbose: print more
:returns: [ list of column names assocated with a network ]
|
[
"Returns",
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"list",
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"column",
"names",
"assocated",
"with",
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"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/network.py#L544-L562
|
12,034
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/network.py
|
network.rename
|
def rename(self, name=None, sourceNetwork=None, verbose=False):
"""
Rename an existing network. The SUID of the network is returned
:param name (string): Enter a new title for the network
:param sourceNetwork (string): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value
can also be used to specify the current network.
:param verbose: print more
:returns: SUID of the network is returned
"""
sourceNetwork=check_network(self,sourceNetwork,verbose=verbose)
PARAMS=set_param(["name","sourceNetwork"],[name,sourceNetwork])
response=api(url=self.__url+"/rename", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def rename(self, name=None, sourceNetwork=None, verbose=False):
"""
Rename an existing network. The SUID of the network is returned
:param name (string): Enter a new title for the network
:param sourceNetwork (string): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value
can also be used to specify the current network.
:param verbose: print more
:returns: SUID of the network is returned
"""
sourceNetwork=check_network(self,sourceNetwork,verbose=verbose)
PARAMS=set_param(["name","sourceNetwork"],[name,sourceNetwork])
response=api(url=self.__url+"/rename", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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Rename an existing network. The SUID of the network is returned
:param name (string): Enter a new title for the network
:param sourceNetwork (string): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value
can also be used to specify the current network.
:param verbose: print more
:returns: SUID of the network is returned
|
[
"Rename",
"an",
"existing",
"network",
".",
"The",
"SUID",
"of",
"the",
"network",
"is",
"returned"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/network.py#L619-L634
|
12,035
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/session.py
|
session.new
|
def new(self, verbose=False):
"""
Destroys the current session and creates a new, empty one.
:param wid: Window ID
:param verbose: print more
"""
response=api(url=self.__url+"/new", verbose=verbose)
return response
|
python
|
def new(self, verbose=False):
"""
Destroys the current session and creates a new, empty one.
:param wid: Window ID
:param verbose: print more
"""
response=api(url=self.__url+"/new", verbose=verbose)
return response
|
[
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"__url",
"+",
"\"/new\"",
",",
"verbose",
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")",
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] |
Destroys the current session and creates a new, empty one.
:param wid: Window ID
:param verbose: print more
|
[
"Destroys",
"the",
"current",
"session",
"and",
"creates",
"a",
"new",
"empty",
"one",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/session.py#L14-L23
|
12,036
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/session.py
|
session.open
|
def open(self, session_file=None,session_url=None, verbose=False):
"""
Opens a session from a local file or URL.
:param session_file: The path to the session file (.cys) to be loaded.
:param session_url: A URL that provides a session file.
:param verbose: print more
"""
PARAMS=set_param(["file", "url"],[session_file, session_url])
response=api(url=self.__url+"/open", PARAMS=PARAMS, verbose=verbose)
return response
|
python
|
def open(self, session_file=None,session_url=None, verbose=False):
"""
Opens a session from a local file or URL.
:param session_file: The path to the session file (.cys) to be loaded.
:param session_url: A URL that provides a session file.
:param verbose: print more
"""
PARAMS=set_param(["file", "url"],[session_file, session_url])
response=api(url=self.__url+"/open", PARAMS=PARAMS, verbose=verbose)
return response
|
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Opens a session from a local file or URL.
:param session_file: The path to the session file (.cys) to be loaded.
:param session_url: A URL that provides a session file.
:param verbose: print more
|
[
"Opens",
"a",
"session",
"from",
"a",
"local",
"file",
"or",
"URL",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/session.py#L26-L37
|
12,037
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/session.py
|
session.save
|
def save(self, session_file, verbose=False):
"""
Saves the current session to an existing file, which will be replaced.
If this is a new session that has not been saved yet, use 'save as'
instead.
:param session_file: The path to the file where the current session
must be saved to.
:param verbose: print more
"""
PARAMS={"file":session_file}
response=api(url=self.__url+"/save", PARAMS=PARAMS, verbose=verbose)
return response
|
python
|
def save(self, session_file, verbose=False):
"""
Saves the current session to an existing file, which will be replaced.
If this is a new session that has not been saved yet, use 'save as'
instead.
:param session_file: The path to the file where the current session
must be saved to.
:param verbose: print more
"""
PARAMS={"file":session_file}
response=api(url=self.__url+"/save", PARAMS=PARAMS, verbose=verbose)
return response
|
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Saves the current session to an existing file, which will be replaced.
If this is a new session that has not been saved yet, use 'save as'
instead.
:param session_file: The path to the file where the current session
must be saved to.
:param verbose: print more
|
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] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/session.py#L40-L54
|
12,038
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/vizmap.py
|
vizmap.apply
|
def apply(self, styles=None, verbose=False):
"""
Applies the specified style to the selected views and returns the
SUIDs of the affected views.
:param styles (string): Name of Style to be applied to the selected
views. = ['Directed', 'BioPAX_SIF', 'Bridging Reads Histogram:unique_0',
'PSIMI 25 Style', 'Coverage Histogram:best&unique', 'Minimal',
'Bridging Reads Histogram:best&unique_0', 'Coverage Histogram_0',
'Big Labels', 'No Histogram:best&unique_0', 'Bridging Reads Histogram:best',
'No Histogram_0', 'No Histogram:best&unique', 'Bridging Reads Histogram_0',
'Ripple', 'Coverage Histogram:unique_0', 'Nested Network Style',
'Coverage Histogram:best', 'Coverage Histogram:best&unique_0',
'default black', 'No Histogram:best_0', 'No Histogram:unique',
'No Histogram:unique_0', 'Solid', 'Bridging Reads Histogram:unique',
'No Histogram:best', 'Coverage Histogram', 'BioPAX', 'Bridging Reads Histogram',
'Coverage Histogram:best_0', 'Sample1', 'Universe', 'Bridging Reads Histogram:best_0',
'Coverage Histogram:unique', 'Bridging Reads Histogram:best&unique',
'No Histogram', 'default']
:param verbose: print more
:returns: SUIDs of the affected views
"""
PARAMS=set_param(["styles"],[styles])
response=api(url=self.__url+"/apply", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def apply(self, styles=None, verbose=False):
"""
Applies the specified style to the selected views and returns the
SUIDs of the affected views.
:param styles (string): Name of Style to be applied to the selected
views. = ['Directed', 'BioPAX_SIF', 'Bridging Reads Histogram:unique_0',
'PSIMI 25 Style', 'Coverage Histogram:best&unique', 'Minimal',
'Bridging Reads Histogram:best&unique_0', 'Coverage Histogram_0',
'Big Labels', 'No Histogram:best&unique_0', 'Bridging Reads Histogram:best',
'No Histogram_0', 'No Histogram:best&unique', 'Bridging Reads Histogram_0',
'Ripple', 'Coverage Histogram:unique_0', 'Nested Network Style',
'Coverage Histogram:best', 'Coverage Histogram:best&unique_0',
'default black', 'No Histogram:best_0', 'No Histogram:unique',
'No Histogram:unique_0', 'Solid', 'Bridging Reads Histogram:unique',
'No Histogram:best', 'Coverage Histogram', 'BioPAX', 'Bridging Reads Histogram',
'Coverage Histogram:best_0', 'Sample1', 'Universe', 'Bridging Reads Histogram:best_0',
'Coverage Histogram:unique', 'Bridging Reads Histogram:best&unique',
'No Histogram', 'default']
:param verbose: print more
:returns: SUIDs of the affected views
"""
PARAMS=set_param(["styles"],[styles])
response=api(url=self.__url+"/apply", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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",",
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] |
Applies the specified style to the selected views and returns the
SUIDs of the affected views.
:param styles (string): Name of Style to be applied to the selected
views. = ['Directed', 'BioPAX_SIF', 'Bridging Reads Histogram:unique_0',
'PSIMI 25 Style', 'Coverage Histogram:best&unique', 'Minimal',
'Bridging Reads Histogram:best&unique_0', 'Coverage Histogram_0',
'Big Labels', 'No Histogram:best&unique_0', 'Bridging Reads Histogram:best',
'No Histogram_0', 'No Histogram:best&unique', 'Bridging Reads Histogram_0',
'Ripple', 'Coverage Histogram:unique_0', 'Nested Network Style',
'Coverage Histogram:best', 'Coverage Histogram:best&unique_0',
'default black', 'No Histogram:best_0', 'No Histogram:unique',
'No Histogram:unique_0', 'Solid', 'Bridging Reads Histogram:unique',
'No Histogram:best', 'Coverage Histogram', 'BioPAX', 'Bridging Reads Histogram',
'Coverage Histogram:best_0', 'Sample1', 'Universe', 'Bridging Reads Histogram:best_0',
'Coverage Histogram:unique', 'Bridging Reads Histogram:best&unique',
'No Histogram', 'default']
:param verbose: print more
:returns: SUIDs of the affected views
|
[
"Applies",
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"style",
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"the",
"selected",
"views",
"and",
"returns",
"the",
"SUIDs",
"of",
"the",
"affected",
"views",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/vizmap.py#L13-L39
|
12,039
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/vizmap.py
|
vizmap.create_style
|
def create_style(self,title=None,defaults=None,mappings=None,verbose=VERBOSE):
"""
Creates a new visual style
:param title: title of the visual style
:param defaults: a list of dictionaries for each visualProperty
:param mappings: a list of dictionaries for each visualProperty
:param host: cytoscape host address, default=cytoscape_host
:param port: cytoscape port, default=1234
:returns: nothing
"""
u=self.__url
host=u.split("//")[1].split(":")[0]
port=u.split(":")[2].split("/")[0]
version=u.split(":")[2].split("/")[1]
if defaults:
defaults_=[]
for d in defaults:
if d:
defaults_.append(d)
defaults=defaults_
if mappings:
mappings_=[]
for m in mappings:
if m:
mappings_.append(m)
mappings=mappings_
try:
update_style(title=title,defaults=defaults,mappings=mappings,host=host,port=port)
print("Existing style was updated.")
sys.stdout.flush()
except:
print("Creating new style.")
sys.stdout.flush()
URL="http://"+str(host)+":"+str(port)+"/v1/styles"
PARAMS={"title":title,\
"defaults":defaults,\
"mappings":mappings}
r = requests.post(url = URL, json = PARAMS)
checkresponse(r)
|
python
|
def create_style(self,title=None,defaults=None,mappings=None,verbose=VERBOSE):
"""
Creates a new visual style
:param title: title of the visual style
:param defaults: a list of dictionaries for each visualProperty
:param mappings: a list of dictionaries for each visualProperty
:param host: cytoscape host address, default=cytoscape_host
:param port: cytoscape port, default=1234
:returns: nothing
"""
u=self.__url
host=u.split("//")[1].split(":")[0]
port=u.split(":")[2].split("/")[0]
version=u.split(":")[2].split("/")[1]
if defaults:
defaults_=[]
for d in defaults:
if d:
defaults_.append(d)
defaults=defaults_
if mappings:
mappings_=[]
for m in mappings:
if m:
mappings_.append(m)
mappings=mappings_
try:
update_style(title=title,defaults=defaults,mappings=mappings,host=host,port=port)
print("Existing style was updated.")
sys.stdout.flush()
except:
print("Creating new style.")
sys.stdout.flush()
URL="http://"+str(host)+":"+str(port)+"/v1/styles"
PARAMS={"title":title,\
"defaults":defaults,\
"mappings":mappings}
r = requests.post(url = URL, json = PARAMS)
checkresponse(r)
|
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"url",
"=",
"URL",
",",
"json",
"=",
"PARAMS",
")",
"checkresponse",
"(",
"r",
")"
] |
Creates a new visual style
:param title: title of the visual style
:param defaults: a list of dictionaries for each visualProperty
:param mappings: a list of dictionaries for each visualProperty
:param host: cytoscape host address, default=cytoscape_host
:param port: cytoscape port, default=1234
:returns: nothing
|
[
"Creates",
"a",
"new",
"visual",
"style"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/vizmap.py#L86-L129
|
12,040
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/vizmap.py
|
vizmap.update_style
|
def update_style(self, title=None,defaults=None,mappings=None, verbose=False):
"""
Updates a visual style
:param title: title of the visual style
:param defaults: a list of dictionaries for each visualProperty
:param mappings: a list of dictionaries for each visualProperty
:returns: nothing
"""
u=self.__url
host=u.split("//")[1].split(":")[0]
port=u.split(":")[2].split("/")[0]
version=u.split(":")[2].split("/")[1]
if defaults:
defaults_=[]
for d in defaults:
if d:
defaults_.append(d)
defaults=defaults_
if mappings:
mappings_=[]
for m in mappings:
if m:
mappings_.append(m)
mappings=mappings_
URL="http://"+str(host)+":"+str(port)+"/v1/styles/"+str(title)
if verbose:
print(URL)
sys.stdout.flush()
response = requests.get(URL).json()
olddefaults=response["defaults"]
oldmappings=response["mappings"]
if mappings:
mappings_visual_properties=[ m["visualProperty"] for m in mappings ]
newmappings=[ m for m in oldmappings if m["visualProperty"] not in mappings_visual_properties ]
for m in mappings:
newmappings.append(m)
else:
newmappings=oldmappings
if defaults:
defaults_visual_properties=[ m["visualProperty"] for m in defaults ]
newdefaults=[ m for m in olddefaults if m["visualProperty"] not in defaults_visual_properties ]
for m in defaults:
newdefaults.append(m)
else:
newdefaults=olddefaults
r=requests.delete(URL)
checkresponse(r)
URL="http://"+str(host)+":"+str(port)+"/v1/styles"
PARAMS={"title":title,\
"defaults":newdefaults,\
"mappings":newmappings}
r = requests.post(url = URL, json = PARAMS)
checkresponse(r)
|
python
|
def update_style(self, title=None,defaults=None,mappings=None, verbose=False):
"""
Updates a visual style
:param title: title of the visual style
:param defaults: a list of dictionaries for each visualProperty
:param mappings: a list of dictionaries for each visualProperty
:returns: nothing
"""
u=self.__url
host=u.split("//")[1].split(":")[0]
port=u.split(":")[2].split("/")[0]
version=u.split(":")[2].split("/")[1]
if defaults:
defaults_=[]
for d in defaults:
if d:
defaults_.append(d)
defaults=defaults_
if mappings:
mappings_=[]
for m in mappings:
if m:
mappings_.append(m)
mappings=mappings_
URL="http://"+str(host)+":"+str(port)+"/v1/styles/"+str(title)
if verbose:
print(URL)
sys.stdout.flush()
response = requests.get(URL).json()
olddefaults=response["defaults"]
oldmappings=response["mappings"]
if mappings:
mappings_visual_properties=[ m["visualProperty"] for m in mappings ]
newmappings=[ m for m in oldmappings if m["visualProperty"] not in mappings_visual_properties ]
for m in mappings:
newmappings.append(m)
else:
newmappings=oldmappings
if defaults:
defaults_visual_properties=[ m["visualProperty"] for m in defaults ]
newdefaults=[ m for m in olddefaults if m["visualProperty"] not in defaults_visual_properties ]
for m in defaults:
newdefaults.append(m)
else:
newdefaults=olddefaults
r=requests.delete(URL)
checkresponse(r)
URL="http://"+str(host)+":"+str(port)+"/v1/styles"
PARAMS={"title":title,\
"defaults":newdefaults,\
"mappings":newmappings}
r = requests.post(url = URL, json = PARAMS)
checkresponse(r)
|
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Updates a visual style
:param title: title of the visual style
:param defaults: a list of dictionaries for each visualProperty
:param mappings: a list of dictionaries for each visualProperty
:returns: nothing
|
[
"Updates",
"a",
"visual",
"style"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/vizmap.py#L131-L194
|
12,041
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/vizmap.py
|
vizmap.simple_defaults
|
def simple_defaults(self, defaults_dic):
"""
Simplifies defaults.
:param defaults_dic: a dictionary of the form { visualProperty_A:value_A, visualProperty_B:value_B, ..}
:returns: a list of dictionaries with each item corresponding to a given key in defaults_dic
"""
defaults=[]
for d in defaults_dic.keys():
dic={}
dic["visualProperty"]=d
dic["value"]=defaults_dic[d]
defaults.append(dic)
return defaults
|
python
|
def simple_defaults(self, defaults_dic):
"""
Simplifies defaults.
:param defaults_dic: a dictionary of the form { visualProperty_A:value_A, visualProperty_B:value_B, ..}
:returns: a list of dictionaries with each item corresponding to a given key in defaults_dic
"""
defaults=[]
for d in defaults_dic.keys():
dic={}
dic["visualProperty"]=d
dic["value"]=defaults_dic[d]
defaults.append(dic)
return defaults
|
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Simplifies defaults.
:param defaults_dic: a dictionary of the form { visualProperty_A:value_A, visualProperty_B:value_B, ..}
:returns: a list of dictionaries with each item corresponding to a given key in defaults_dic
|
[
"Simplifies",
"defaults",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/vizmap.py#L278-L293
|
12,042
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.attribute_circle
|
def attribute_circle(self, EdgeAttribute=None, network=None, \
NodeAttribute=None, nodeList=None, singlePartition=None,\
spacing=None, verbose=False):
"""
Execute the Attribute Circle Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The
keywords all, selected, or unselected can be used to specify nodes
by their selection state. The pattern COLUMN:VALUE sets this parameter
to any rows that contain the specified column value; if the COLUMN
prefix is not used, the NAME column is matched by default. A list of
COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,...
can be used to match multiple values.
:param singlePartition (string, optional): Don't partition graph before
layout, only boolean values allowed: true or false
:param spacing (string, optional): Circle size, in numeric value
:param verbose: print more
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["EdgeAttribute","network","NodeAttribute","nodeList","singlePartition","spacing"],\
[EdgeAttribute,network,NodeAttribute,nodeList,singlePartition,spacing])
response=api(url=self.__url+"/attribute-circle", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def attribute_circle(self, EdgeAttribute=None, network=None, \
NodeAttribute=None, nodeList=None, singlePartition=None,\
spacing=None, verbose=False):
"""
Execute the Attribute Circle Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The
keywords all, selected, or unselected can be used to specify nodes
by their selection state. The pattern COLUMN:VALUE sets this parameter
to any rows that contain the specified column value; if the COLUMN
prefix is not used, the NAME column is matched by default. A list of
COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,...
can be used to match multiple values.
:param singlePartition (string, optional): Don't partition graph before
layout, only boolean values allowed: true or false
:param spacing (string, optional): Circle size, in numeric value
:param verbose: print more
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["EdgeAttribute","network","NodeAttribute","nodeList","singlePartition","spacing"],\
[EdgeAttribute,network,NodeAttribute,nodeList,singlePartition,spacing])
response=api(url=self.__url+"/attribute-circle", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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"\"POST\"",
",",
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"verbose",
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"response"
] |
Execute the Attribute Circle Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The
keywords all, selected, or unselected can be used to specify nodes
by their selection state. The pattern COLUMN:VALUE sets this parameter
to any rows that contain the specified column value; if the COLUMN
prefix is not used, the NAME column is matched by default. A list of
COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,...
can be used to match multiple values.
:param singlePartition (string, optional): Don't partition graph before
layout, only boolean values allowed: true or false
:param spacing (string, optional): Circle size, in numeric value
:param verbose: print more
|
[
"Execute",
"the",
"Attribute",
"Circle",
"Layout",
"on",
"a",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L29-L61
|
12,043
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.attributes_layout
|
def attributes_layout(self, EdgeAttribute=None, maxwidth=None, minrad=None, \
network=None, NodeAttribute=None,nodeList=None, radmult=None, \
spacingx=None, spacingy=None, verbose=False):
"""
Execute the Group Attributes Layout on a network
:param EdgeAttribute (string, optional): The name of the edge column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param maxwidth (string, optional): Maximum width of a row, in numeric value
:param minrad (string, optional): Minimum width of a partition, in
numeric value
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The
keywords all, selected, or unselected can be used to specify nodes
by their selection state. The pattern COLUMN:VALUE sets this parameter
to any rows that contain the specified column value; if the COLUMN
prefix is not used, the NAME column is matched by default. A list
of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,...
can be used to match multiple values.
:param radmult (string, optional): Minimum width of a partition, in
numeric value
:param spacingx (string, optional): Horizontal spacing between two
partitions in a row, in numeric value
:param spacingy (string, optional): Vertical spacing between the largest
partitions of two rows, in numeric value
:param verbose: print more
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["EdgeAttribute","network","NodeAttribute","nodeList","singlePartition","spacing"],\
[EdgeAttribute, maxwidth, \
minrad, network, NodeAttribute,nodeList, radmult, \
spacingx, spacingy])
response=api(url=self.__url+"/attributes-layout", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def attributes_layout(self, EdgeAttribute=None, maxwidth=None, minrad=None, \
network=None, NodeAttribute=None,nodeList=None, radmult=None, \
spacingx=None, spacingy=None, verbose=False):
"""
Execute the Group Attributes Layout on a network
:param EdgeAttribute (string, optional): The name of the edge column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param maxwidth (string, optional): Maximum width of a row, in numeric value
:param minrad (string, optional): Minimum width of a partition, in
numeric value
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The
keywords all, selected, or unselected can be used to specify nodes
by their selection state. The pattern COLUMN:VALUE sets this parameter
to any rows that contain the specified column value; if the COLUMN
prefix is not used, the NAME column is matched by default. A list
of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,...
can be used to match multiple values.
:param radmult (string, optional): Minimum width of a partition, in
numeric value
:param spacingx (string, optional): Horizontal spacing between two
partitions in a row, in numeric value
:param spacingy (string, optional): Vertical spacing between the largest
partitions of two rows, in numeric value
:param verbose: print more
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["EdgeAttribute","network","NodeAttribute","nodeList","singlePartition","spacing"],\
[EdgeAttribute, maxwidth, \
minrad, network, NodeAttribute,nodeList, radmult, \
spacingx, spacingy])
response=api(url=self.__url+"/attributes-layout", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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] |
Execute the Group Attributes Layout on a network
:param EdgeAttribute (string, optional): The name of the edge column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param maxwidth (string, optional): Maximum width of a row, in numeric value
:param minrad (string, optional): Minimum width of a partition, in
numeric value
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column
containing numeric values that will be used as weights in the layout
algorithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The
keywords all, selected, or unselected can be used to specify nodes
by their selection state. The pattern COLUMN:VALUE sets this parameter
to any rows that contain the specified column value; if the COLUMN
prefix is not used, the NAME column is matched by default. A list
of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,...
can be used to match multiple values.
:param radmult (string, optional): Minimum width of a partition, in
numeric value
:param spacingx (string, optional): Horizontal spacing between two
partitions in a row, in numeric value
:param spacingy (string, optional): Vertical spacing between the largest
partitions of two rows, in numeric value
:param verbose: print more
|
[
"Execute",
"the",
"Group",
"Attributes",
"Layout",
"on",
"a",
"network"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L64-L104
|
12,044
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.circular
|
def circular(self,EdgeAttribute=None,leftEdge=None,network=None,\
NodeAttribute=None,nodeHorizontalSpacing=None,nodeList=None,\
nodeVerticalSpacing=None,rightMargin=None,singlePartition=None,topEdge=None,\
verbose=None):
"""
Execute the Circular Layout on a network
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param leftEdge (string, optional): Left edge margin, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
:param rightMargin (string, optional): Right edge margin, in numeric value
:param singlePartition (string, optional): Don't partition graph before lay
out; only boolean values are allowed: true or false
:param topEdge (string, optional): Top edge margin, in numeric value
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['EdgeAttribute','leftEdge','network','NodeAttribute',\
'nodeHorizontalSpacing','nodeList','nodeVerticalSpacing','rightMargin',\
'singlePartition','topEdge'],[EdgeAttribute,leftEdge,network,NodeAttribute,\
nodeHorizontalSpacing,nodeList,nodeVerticalSpacing,rightMargin,\
singlePartition,topEdge])
response=api(url=self.__url+"/circular", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def circular(self,EdgeAttribute=None,leftEdge=None,network=None,\
NodeAttribute=None,nodeHorizontalSpacing=None,nodeList=None,\
nodeVerticalSpacing=None,rightMargin=None,singlePartition=None,topEdge=None,\
verbose=None):
"""
Execute the Circular Layout on a network
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param leftEdge (string, optional): Left edge margin, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
:param rightMargin (string, optional): Right edge margin, in numeric value
:param singlePartition (string, optional): Don't partition graph before lay
out; only boolean values are allowed: true or false
:param topEdge (string, optional): Top edge margin, in numeric value
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['EdgeAttribute','leftEdge','network','NodeAttribute',\
'nodeHorizontalSpacing','nodeList','nodeVerticalSpacing','rightMargin',\
'singlePartition','topEdge'],[EdgeAttribute,leftEdge,network,NodeAttribute,\
nodeHorizontalSpacing,nodeList,nodeVerticalSpacing,rightMargin,\
singlePartition,topEdge])
response=api(url=self.__url+"/circular", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Execute the Circular Layout on a network
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param leftEdge (string, optional): Left edge margin, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
:param rightMargin (string, optional): Right edge margin, in numeric value
:param singlePartition (string, optional): Don't partition graph before lay
out; only boolean values are allowed: true or false
:param topEdge (string, optional): Top edge margin, in numeric value
|
[
"Execute",
"the",
"Circular",
"Layout",
"on",
"a",
"network"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L106-L146
|
12,045
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.copycat
|
def copycat(self,gridUnmapped=None,selectUnmapped=None,sourceColumn=None,\
sourceNetwork=None,targetColumn=None,targetNetwork=None,verbose=None):
"""
Sets the coordinates for each node in the target network to the coordinates
of a matching node in the source network.
Optional parameters such as gridUnmapped and selectUnmapped determine
the behavior of target network nodes that could not be matched.
:param gridUnmapped (string, optional): If this is set to true, any nodes i
n the target network that could not be matched to a node in the sour
ce network will be laid out in a grid
:param selectUnmapped (string, optional): If this is set to true, any nodes
in the target network that could not be matched to a node in the so
urce network will be selected in the target network
:param sourceColumn (string): The name of column in the node table used to
match nodes
:param sourceNetwork (string): The name of network to get node coordinates
from
:param targetColumn (string): The name of column in the node table used to
match nodes
:param targetNetwork (string): The name of the network to apply coordinates
to.
"""
PARAMS=set_param(['gridUnmapped','selectUnmapped','sourceColumn',\
'sourceNetwork','targetColumn','targetNetwork'],[gridUnmapped,\
selectUnmapped,sourceColumn,sourceNetwork,targetColumn,targetNetwork])
response=api(url=self.__url+"/copycat", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def copycat(self,gridUnmapped=None,selectUnmapped=None,sourceColumn=None,\
sourceNetwork=None,targetColumn=None,targetNetwork=None,verbose=None):
"""
Sets the coordinates for each node in the target network to the coordinates
of a matching node in the source network.
Optional parameters such as gridUnmapped and selectUnmapped determine
the behavior of target network nodes that could not be matched.
:param gridUnmapped (string, optional): If this is set to true, any nodes i
n the target network that could not be matched to a node in the sour
ce network will be laid out in a grid
:param selectUnmapped (string, optional): If this is set to true, any nodes
in the target network that could not be matched to a node in the so
urce network will be selected in the target network
:param sourceColumn (string): The name of column in the node table used to
match nodes
:param sourceNetwork (string): The name of network to get node coordinates
from
:param targetColumn (string): The name of column in the node table used to
match nodes
:param targetNetwork (string): The name of the network to apply coordinates
to.
"""
PARAMS=set_param(['gridUnmapped','selectUnmapped','sourceColumn',\
'sourceNetwork','targetColumn','targetNetwork'],[gridUnmapped,\
selectUnmapped,sourceColumn,sourceNetwork,targetColumn,targetNetwork])
response=api(url=self.__url+"/copycat", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
"def",
"copycat",
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"self",
",",
"gridUnmapped",
"=",
"None",
",",
"selectUnmapped",
"=",
"None",
",",
"sourceColumn",
"=",
"None",
",",
"sourceNetwork",
"=",
"None",
",",
"targetColumn",
"=",
"None",
",",
"targetNetwork",
"=",
"None",
",",
"verbose",
"=",
"None",
")",
":",
"PARAMS",
"=",
"set_param",
"(",
"[",
"'gridUnmapped'",
",",
"'selectUnmapped'",
",",
"'sourceColumn'",
",",
"'sourceNetwork'",
",",
"'targetColumn'",
",",
"'targetNetwork'",
"]",
",",
"[",
"gridUnmapped",
",",
"selectUnmapped",
",",
"sourceColumn",
",",
"sourceNetwork",
",",
"targetColumn",
",",
"targetNetwork",
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"api",
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"url",
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"self",
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"__url",
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"\"/copycat\"",
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"PARAMS",
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"PARAMS",
",",
"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Sets the coordinates for each node in the target network to the coordinates
of a matching node in the source network.
Optional parameters such as gridUnmapped and selectUnmapped determine
the behavior of target network nodes that could not be matched.
:param gridUnmapped (string, optional): If this is set to true, any nodes i
n the target network that could not be matched to a node in the sour
ce network will be laid out in a grid
:param selectUnmapped (string, optional): If this is set to true, any nodes
in the target network that could not be matched to a node in the so
urce network will be selected in the target network
:param sourceColumn (string): The name of column in the node table used to
match nodes
:param sourceNetwork (string): The name of network to get node coordinates
from
:param targetColumn (string): The name of column in the node table used to
match nodes
:param targetNetwork (string): The name of the network to apply coordinates
to.
|
[
"Sets",
"the",
"coordinates",
"for",
"each",
"node",
"in",
"the",
"target",
"network",
"to",
"the",
"coordinates",
"of",
"a",
"matching",
"node",
"in",
"the",
"source",
"network",
".",
"Optional",
"parameters",
"such",
"as",
"gridUnmapped",
"and",
"selectUnmapped",
"determine",
"the",
"behavior",
"of",
"target",
"network",
"nodes",
"that",
"could",
"not",
"be",
"matched",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L148-L175
|
12,046
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.degree_circle
|
def degree_circle(self,EdgeAttribute=None,network=None,NodeAttribute=None,\
nodeList=None,singlePartition=None,verbose=None):
"""
Execute the Degree Sorted Circle Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['EdgeAttribute','network','NodeAttribute','nodeList',\
'singlePartition'],[EdgeAttribute,network,NodeAttribute,nodeList,\
singlePartition])
response=api(url=self.__url+"/degree-circle", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def degree_circle(self,EdgeAttribute=None,network=None,NodeAttribute=None,\
nodeList=None,singlePartition=None,verbose=None):
"""
Execute the Degree Sorted Circle Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['EdgeAttribute','network','NodeAttribute','nodeList',\
'singlePartition'],[EdgeAttribute,network,NodeAttribute,nodeList,\
singlePartition])
response=api(url=self.__url+"/degree-circle", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
"def",
"degree_circle",
"(",
"self",
",",
"EdgeAttribute",
"=",
"None",
",",
"network",
"=",
"None",
",",
"NodeAttribute",
"=",
"None",
",",
"nodeList",
"=",
"None",
",",
"singlePartition",
"=",
"None",
",",
"verbose",
"=",
"None",
")",
":",
"network",
"=",
"check_network",
"(",
"self",
",",
"network",
",",
"verbose",
"=",
"verbose",
")",
"PARAMS",
"=",
"set_param",
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"[",
"'EdgeAttribute'",
",",
"'network'",
",",
"'NodeAttribute'",
",",
"'nodeList'",
",",
"'singlePartition'",
"]",
",",
"[",
"EdgeAttribute",
",",
"network",
",",
"NodeAttribute",
",",
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",",
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"]",
")",
"response",
"=",
"api",
"(",
"url",
"=",
"self",
".",
"__url",
"+",
"\"/degree-circle\"",
",",
"PARAMS",
"=",
"PARAMS",
",",
"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Execute the Degree Sorted Circle Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
|
[
"Execute",
"the",
"Degree",
"Sorted",
"Circle",
"Layout",
"on",
"a",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L233-L262
|
12,047
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.force_directed
|
def force_directed(self,defaultEdgeWeight=None,defaultNodeMass=None,\
defaultSpringCoefficient=None,defaultSpringLength=None,EdgeAttribute=None,\
isDeterministic=None,maxWeightCutoff=None,minWeightCutoff=None,network=None,\
NodeAttribute=None,nodeList=None,numIterations=None,singlePartition=None,\
Type=None,verbose=None):
"""
Execute the Prefuse Force Directed Layout on a network
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param defaultNodeMass (string, optional): Default Node Mass, in numeric va
lue
:param defaultSpringCoefficient (string, optional): Default Spring Coeffici
ent, in numeric value
:param defaultSpringLength (string, optional): Default Spring Length, in nu
meric value
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param isDeterministic (string, optional): Force deterministic layouts (slo
wer); boolean values only, true or false; defaults to false
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param numIterations (string, optional): Number of Iterations, in numeric v
alue
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['defaultEdgeWeight','defaultNodeMass','defaultSpringCoefficient',\
'defaultSpringLength','EdgeAttribute','isDeterministic','maxWeightCutoff',\
'minWeightCutoff','network','NodeAttribute','nodeList','numIterations',\
'singlePartition','Type'],[defaultEdgeWeight,defaultNodeMass,\
defaultSpringCoefficient,defaultSpringLength,EdgeAttribute,isDeterministic,\
maxWeightCutoff,minWeightCutoff,network,NodeAttribute,nodeList,numIterations,\
singlePartition,Type])
response=api(url=self.__url+"/force-directed", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def force_directed(self,defaultEdgeWeight=None,defaultNodeMass=None,\
defaultSpringCoefficient=None,defaultSpringLength=None,EdgeAttribute=None,\
isDeterministic=None,maxWeightCutoff=None,minWeightCutoff=None,network=None,\
NodeAttribute=None,nodeList=None,numIterations=None,singlePartition=None,\
Type=None,verbose=None):
"""
Execute the Prefuse Force Directed Layout on a network
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param defaultNodeMass (string, optional): Default Node Mass, in numeric va
lue
:param defaultSpringCoefficient (string, optional): Default Spring Coeffici
ent, in numeric value
:param defaultSpringLength (string, optional): Default Spring Length, in nu
meric value
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param isDeterministic (string, optional): Force deterministic layouts (slo
wer); boolean values only, true or false; defaults to false
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param numIterations (string, optional): Number of Iterations, in numeric v
alue
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['defaultEdgeWeight','defaultNodeMass','defaultSpringCoefficient',\
'defaultSpringLength','EdgeAttribute','isDeterministic','maxWeightCutoff',\
'minWeightCutoff','network','NodeAttribute','nodeList','numIterations',\
'singlePartition','Type'],[defaultEdgeWeight,defaultNodeMass,\
defaultSpringCoefficient,defaultSpringLength,EdgeAttribute,isDeterministic,\
maxWeightCutoff,minWeightCutoff,network,NodeAttribute,nodeList,numIterations,\
singlePartition,Type])
response=api(url=self.__url+"/force-directed", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
"def",
"force_directed",
"(",
"self",
",",
"defaultEdgeWeight",
"=",
"None",
",",
"defaultNodeMass",
"=",
"None",
",",
"defaultSpringCoefficient",
"=",
"None",
",",
"defaultSpringLength",
"=",
"None",
",",
"EdgeAttribute",
"=",
"None",
",",
"isDeterministic",
"=",
"None",
",",
"maxWeightCutoff",
"=",
"None",
",",
"minWeightCutoff",
"=",
"None",
",",
"network",
"=",
"None",
",",
"NodeAttribute",
"=",
"None",
",",
"nodeList",
"=",
"None",
",",
"numIterations",
"=",
"None",
",",
"singlePartition",
"=",
"None",
",",
"Type",
"=",
"None",
",",
"verbose",
"=",
"None",
")",
":",
"network",
"=",
"check_network",
"(",
"self",
",",
"network",
",",
"verbose",
"=",
"verbose",
")",
"PARAMS",
"=",
"set_param",
"(",
"[",
"'defaultEdgeWeight'",
",",
"'defaultNodeMass'",
",",
"'defaultSpringCoefficient'",
",",
"'defaultSpringLength'",
",",
"'EdgeAttribute'",
",",
"'isDeterministic'",
",",
"'maxWeightCutoff'",
",",
"'minWeightCutoff'",
",",
"'network'",
",",
"'NodeAttribute'",
",",
"'nodeList'",
",",
"'numIterations'",
",",
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",",
"'Type'",
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",",
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"defaultEdgeWeight",
",",
"defaultNodeMass",
",",
"defaultSpringCoefficient",
",",
"defaultSpringLength",
",",
"EdgeAttribute",
",",
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",",
"maxWeightCutoff",
",",
"minWeightCutoff",
",",
"network",
",",
"NodeAttribute",
",",
"nodeList",
",",
"numIterations",
",",
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",",
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")",
"response",
"=",
"api",
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"url",
"=",
"self",
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"__url",
"+",
"\"/force-directed\"",
",",
"PARAMS",
"=",
"PARAMS",
",",
"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Execute the Prefuse Force Directed Layout on a network
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param defaultNodeMass (string, optional): Default Node Mass, in numeric va
lue
:param defaultSpringCoefficient (string, optional): Default Spring Coeffici
ent, in numeric value
:param defaultSpringLength (string, optional): Default Spring Length, in nu
meric value
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param isDeterministic (string, optional): Force deterministic layouts (slo
wer); boolean values only, true or false; defaults to false
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param numIterations (string, optional): Number of Iterations, in numeric v
alue
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
|
[
"Execute",
"the",
"Prefuse",
"Force",
"Directed",
"Layout",
"on",
"a",
"network"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L265-L321
|
12,048
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.genemania_force_directed
|
def genemania_force_directed(self,curveSteepness=None,defaultEdgeWeight=None,\
defaultSpringCoefficient=None,defaultSpringLength=None,EdgeAttribute=None,\
ignoreHiddenElements=None,isDeterministic=None,maxNodeMass=None,\
maxWeightCutoff=None,midpointEdges=None,minNodeMass=None,minWeightCutoff=None,\
network=None,NodeAttribute=None,nodeList=None,numIterations=None,\
singlePartition=None,Type=None,verbose=None):
"""
Execute the GeneMANIA Force Directed Layout on a network.
:param curveSteepness (string, optional):
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param defaultSpringCoefficient (string, optional):
:param defaultSpringLength (string, optional):
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param ignoreHiddenElements (string, optional):
:param isDeterministic (string, optional):
:param maxNodeMass (string, optional):
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param midpointEdges (string, optional):
:param minNodeMass (string, optional):
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param numIterations (string, optional):
:param singlePartition (string, optional):
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['curveSteepness','defaultEdgeWeight',\
'defaultSpringCoefficient','defaultSpringLength','EdgeAttribute',\
'ignoreHiddenElements','isDeterministic','maxNodeMass','maxWeightCutoff',\
'midpointEdges','minNodeMass','minWeightCutoff','network','NodeAttribute',\
'nodeList','numIterations','singlePartition','Type'],[curveSteepness,\
defaultEdgeWeight,defaultSpringCoefficient,defaultSpringLength,EdgeAttribute,\
ignoreHiddenElements,isDeterministic,maxNodeMass,maxWeightCutoff,\
midpointEdges,minNodeMass,minWeightCutoff,network,NodeAttribute,nodeList,\
numIterations,singlePartition,Type])
response=api(url=self.__url+"/genemania-force-directed", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def genemania_force_directed(self,curveSteepness=None,defaultEdgeWeight=None,\
defaultSpringCoefficient=None,defaultSpringLength=None,EdgeAttribute=None,\
ignoreHiddenElements=None,isDeterministic=None,maxNodeMass=None,\
maxWeightCutoff=None,midpointEdges=None,minNodeMass=None,minWeightCutoff=None,\
network=None,NodeAttribute=None,nodeList=None,numIterations=None,\
singlePartition=None,Type=None,verbose=None):
"""
Execute the GeneMANIA Force Directed Layout on a network.
:param curveSteepness (string, optional):
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param defaultSpringCoefficient (string, optional):
:param defaultSpringLength (string, optional):
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param ignoreHiddenElements (string, optional):
:param isDeterministic (string, optional):
:param maxNodeMass (string, optional):
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param midpointEdges (string, optional):
:param minNodeMass (string, optional):
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param numIterations (string, optional):
:param singlePartition (string, optional):
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['curveSteepness','defaultEdgeWeight',\
'defaultSpringCoefficient','defaultSpringLength','EdgeAttribute',\
'ignoreHiddenElements','isDeterministic','maxNodeMass','maxWeightCutoff',\
'midpointEdges','minNodeMass','minWeightCutoff','network','NodeAttribute',\
'nodeList','numIterations','singlePartition','Type'],[curveSteepness,\
defaultEdgeWeight,defaultSpringCoefficient,defaultSpringLength,EdgeAttribute,\
ignoreHiddenElements,isDeterministic,maxNodeMass,maxWeightCutoff,\
midpointEdges,minNodeMass,minWeightCutoff,network,NodeAttribute,nodeList,\
numIterations,singlePartition,Type])
response=api(url=self.__url+"/genemania-force-directed", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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"=",
"verbose",
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] |
Execute the GeneMANIA Force Directed Layout on a network.
:param curveSteepness (string, optional):
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param defaultSpringCoefficient (string, optional):
:param defaultSpringLength (string, optional):
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param ignoreHiddenElements (string, optional):
:param isDeterministic (string, optional):
:param maxNodeMass (string, optional):
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param midpointEdges (string, optional):
:param minNodeMass (string, optional):
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param numIterations (string, optional):
:param singlePartition (string, optional):
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
|
[
"Execute",
"the",
"GeneMANIA",
"Force",
"Directed",
"Layout",
"on",
"a",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L455-L512
|
12,049
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.get_preferred
|
def get_preferred(self,network=None,verbose=None):
"""
Returns the name of the current preferred layout or empty string if not
set. Default is grid.
:param network (string, optional): Gets the name of the current preferred l
ayout
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['network'],[network])
response=api(url=self.__url+"/get preferred", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def get_preferred(self,network=None,verbose=None):
"""
Returns the name of the current preferred layout or empty string if not
set. Default is grid.
:param network (string, optional): Gets the name of the current preferred l
ayout
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['network'],[network])
response=api(url=self.__url+"/get preferred", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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] |
Returns the name of the current preferred layout or empty string if not
set. Default is grid.
:param network (string, optional): Gets the name of the current preferred l
ayout
|
[
"Returns",
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"layout",
"or",
"empty",
"string",
"if",
"not",
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".",
"Default",
"is",
"grid",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L515-L526
|
12,050
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.grid
|
def grid(self,EdgeAttribute=None,network=None,NodeAttribute=None,\
nodeHorizontalSpacing=None,nodeList=None,nodeVerticalSpacing=None,verbose=None):
"""
Execute the Grid Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['EdgeAttribute','network','NodeAttribute',\
'nodeHorizontalSpacing','nodeList','nodeVerticalSpacing'],\
[EdgeAttribute,network,NodeAttribute,nodeHorizontalSpacing,nodeList,\
nodeVerticalSpacing])
response=api(url=self.__url+"/grid", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def grid(self,EdgeAttribute=None,network=None,NodeAttribute=None,\
nodeHorizontalSpacing=None,nodeList=None,nodeVerticalSpacing=None,verbose=None):
"""
Execute the Grid Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['EdgeAttribute','network','NodeAttribute',\
'nodeHorizontalSpacing','nodeList','nodeVerticalSpacing'],\
[EdgeAttribute,network,NodeAttribute,nodeHorizontalSpacing,nodeList,\
nodeVerticalSpacing])
response=api(url=self.__url+"/grid", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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"nodeHorizontalSpacing",
"=",
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] |
Execute the Grid Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
|
[
"Execute",
"the",
"Grid",
"Layout",
"on",
"a",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L528-L560
|
12,051
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.hierarchical
|
def hierarchical(self,bandGap=None,componentSpacing=None,EdgeAttribute=None,\
leftEdge=None,network=None,NodeAttribute=None,nodeHorizontalSpacing=None,\
nodeList=None,nodeVerticalSpacing=None,rightMargin=None,topEdge=None,\
verbose=None):
"""
Execute the Hierarchical Layout on a network.
:param bandGap (string, optional): Band gap, in numeric value
:param componentSpacing (string, optional): Component spacing, in numeric v
alue
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param leftEdge (string, optional): Left edge margin, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
:param rightMargin (string, optional): Right edge margin, in numeric value
:param topEdge (string, optional): Top edge margin, in numeric value
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['bandGap','componentSpacing','EdgeAttribute','leftEdge',\
'network','NodeAttribute','nodeHorizontalSpacing','nodeList',\
'nodeVerticalSpacing','rightMargin','topEdge'],[bandGap,componentSpacing,\
EdgeAttribute,leftEdge,network,NodeAttribute,nodeHorizontalSpacing,\
nodeList,nodeVerticalSpacing,rightMargin,topEdge])
response=api(url=self.__url+"/hierarchical", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def hierarchical(self,bandGap=None,componentSpacing=None,EdgeAttribute=None,\
leftEdge=None,network=None,NodeAttribute=None,nodeHorizontalSpacing=None,\
nodeList=None,nodeVerticalSpacing=None,rightMargin=None,topEdge=None,\
verbose=None):
"""
Execute the Hierarchical Layout on a network.
:param bandGap (string, optional): Band gap, in numeric value
:param componentSpacing (string, optional): Component spacing, in numeric v
alue
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param leftEdge (string, optional): Left edge margin, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
:param rightMargin (string, optional): Right edge margin, in numeric value
:param topEdge (string, optional): Top edge margin, in numeric value
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['bandGap','componentSpacing','EdgeAttribute','leftEdge',\
'network','NodeAttribute','nodeHorizontalSpacing','nodeList',\
'nodeVerticalSpacing','rightMargin','topEdge'],[bandGap,componentSpacing,\
EdgeAttribute,leftEdge,network,NodeAttribute,nodeHorizontalSpacing,\
nodeList,nodeVerticalSpacing,rightMargin,topEdge])
response=api(url=self.__url+"/hierarchical", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
"def",
"hierarchical",
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"self",
",",
"bandGap",
"=",
"None",
",",
"componentSpacing",
"=",
"None",
",",
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"=",
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",",
"leftEdge",
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",",
"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Execute the Hierarchical Layout on a network.
:param bandGap (string, optional): Band gap, in numeric value
:param componentSpacing (string, optional): Component spacing, in numeric v
alue
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param leftEdge (string, optional): Left edge margin, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeHorizontalSpacing (string, optional): Horizontal spacing between
nodes, in numeric value
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param nodeVerticalSpacing (string, optional): Vertical spacing between nod
es, in numeric value
:param rightMargin (string, optional): Right edge margin, in numeric value
:param topEdge (string, optional): Top edge margin, in numeric value
|
[
"Execute",
"the",
"Hierarchical",
"Layout",
"on",
"a",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L563-L604
|
12,052
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.isom
|
def isom(self,coolingFactor=None,EdgeAttribute=None,initialAdaptation=None,\
maxEpoch=None,minAdaptation=None,minRadius=None,network=None,NodeAttribute=None,\
nodeList=None,radius=None,radiusConstantTime=None,singlePartition=None,\
sizeFactor=None,verbose=None):
"""
Execute the Inverted Self-Organizing Map Layout on a network.
:param coolingFactor (string, optional): Cooling factor, in numeric value
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param initialAdaptation (string, optional): Initial adaptation, in numeric
value
:param maxEpoch (string, optional): Number of iterations, in numeric value
:param minAdaptation (string, optional): Minimum adaptation value, in numer
ic value
:param minRadius (string, optional): Minimum radius, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param radius (string, optional): Radius, in numeric value
:param radiusConstantTime (string, optional): Radius constant, in numeric v
alue
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param sizeFactor (string, optional): Size factor, in numeric value
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['coolingFactor','EdgeAttribute','initialAdaptation',\
'maxEpoch','minAdaptation','minRadius','network','NodeAttribute','nodeList',\
'radius','radiusConstantTime','singlePartition','sizeFactor'],[coolingFactor,\
EdgeAttribute,initialAdaptation,maxEpoch,minAdaptation,minRadius,network,\
NodeAttribute,nodeList,radius,radiusConstantTime,singlePartition,sizeFactor])
response=api(url=self.__url+"/isom", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def isom(self,coolingFactor=None,EdgeAttribute=None,initialAdaptation=None,\
maxEpoch=None,minAdaptation=None,minRadius=None,network=None,NodeAttribute=None,\
nodeList=None,radius=None,radiusConstantTime=None,singlePartition=None,\
sizeFactor=None,verbose=None):
"""
Execute the Inverted Self-Organizing Map Layout on a network.
:param coolingFactor (string, optional): Cooling factor, in numeric value
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param initialAdaptation (string, optional): Initial adaptation, in numeric
value
:param maxEpoch (string, optional): Number of iterations, in numeric value
:param minAdaptation (string, optional): Minimum adaptation value, in numer
ic value
:param minRadius (string, optional): Minimum radius, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param radius (string, optional): Radius, in numeric value
:param radiusConstantTime (string, optional): Radius constant, in numeric v
alue
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param sizeFactor (string, optional): Size factor, in numeric value
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['coolingFactor','EdgeAttribute','initialAdaptation',\
'maxEpoch','minAdaptation','minRadius','network','NodeAttribute','nodeList',\
'radius','radiusConstantTime','singlePartition','sizeFactor'],[coolingFactor,\
EdgeAttribute,initialAdaptation,maxEpoch,minAdaptation,minRadius,network,\
NodeAttribute,nodeList,radius,radiusConstantTime,singlePartition,sizeFactor])
response=api(url=self.__url+"/isom", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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] |
Execute the Inverted Self-Organizing Map Layout on a network.
:param coolingFactor (string, optional): Cooling factor, in numeric value
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param initialAdaptation (string, optional): Initial adaptation, in numeric
value
:param maxEpoch (string, optional): Number of iterations, in numeric value
:param minAdaptation (string, optional): Minimum adaptation value, in numer
ic value
:param minRadius (string, optional): Minimum radius, in numeric value
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param radius (string, optional): Radius, in numeric value
:param radiusConstantTime (string, optional): Radius constant, in numeric v
alue
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param sizeFactor (string, optional): Size factor, in numeric value
|
[
"Execute",
"the",
"Inverted",
"Self",
"-",
"Organizing",
"Map",
"Layout",
"on",
"a",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L607-L651
|
12,053
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.kamada_kawai
|
def kamada_kawai(self,defaultEdgeWeight=None,EdgeAttribute=None,\
m_anticollisionSpringStrength=None,m_averageIterationsPerNode=None,\
m_disconnectedNodeDistanceSpringRestLength=None,\
m_disconnectedNodeDistanceSpringStrength=None,m_layoutPass=None,\
m_nodeDistanceRestLengthConstant=None,m_nodeDistanceStrengthConstant=None,\
maxWeightCutoff=None,minWeightCutoff=None,network=None,NodeAttribute=None,\
nodeList=None,randomize=None,singlePartition=None,Type=None,unweighted=None,\
verbose=None):
"""
Execute the Edge-weighted Spring Embedded Layout on a network.
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param m_anticollisionSpringStrength (string, optional): Strength to apply
to avoid collisions, in numeric value
:param m_averageIterationsPerNode (string, optional): Average number of ite
ratations for each node, in numeric value
:param m_disconnectedNodeDistanceSpringRestLength (string, optional): Rest
length of a 'disconnected' spring, in numeric value
:param m_disconnectedNodeDistanceSpringStrength (string, optional): Strengt
h of a 'disconnected' spring, in numeric value
:param m_layoutPass (string, optional): Number of layout passes, in numeric
value
:param m_nodeDistanceRestLengthConstant (string, optional): Spring rest len
gth, in numeric value
:param m_nodeDistanceStrengthConstant (string, optional): Spring strength,
in numeric value
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param randomize (string, optional): Randomize graph before layout; boolean
values only, true or false; defaults to true
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
:param unweighted (string, optional): Use unweighted edges; boolean values
only, true or false; defaults to false
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['defaultEdgeWeight','EdgeAttribute',\
'm_anticollisionSpringStrength','m_averageIterationsPerNode',\
'm_disconnectedNodeDistanceSpringRestLength',\
'm_disconnectedNodeDistanceSpringStrength','m_layoutPass',\
'm_nodeDistanceRestLengthConstant','m_nodeDistanceStrengthConstant',\
'maxWeightCutoff','minWeightCutoff','network','NodeAttribute','nodeList',\
'randomize','singlePartition','Type','unweighted'],[defaultEdgeWeight,\
EdgeAttribute,m_anticollisionSpringStrength,m_averageIterationsPerNode,\
m_disconnectedNodeDistanceSpringRestLength,\
m_disconnectedNodeDistanceSpringStrength,m_layoutPass,\
m_nodeDistanceRestLengthConstant,m_nodeDistanceStrengthConstant,\
maxWeightCutoff,minWeightCutoff,network,NodeAttribute,nodeList,randomize,\
singlePartition,Type,unweighted])
response=api(url=self.__url+"/kamada-kawai", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def kamada_kawai(self,defaultEdgeWeight=None,EdgeAttribute=None,\
m_anticollisionSpringStrength=None,m_averageIterationsPerNode=None,\
m_disconnectedNodeDistanceSpringRestLength=None,\
m_disconnectedNodeDistanceSpringStrength=None,m_layoutPass=None,\
m_nodeDistanceRestLengthConstant=None,m_nodeDistanceStrengthConstant=None,\
maxWeightCutoff=None,minWeightCutoff=None,network=None,NodeAttribute=None,\
nodeList=None,randomize=None,singlePartition=None,Type=None,unweighted=None,\
verbose=None):
"""
Execute the Edge-weighted Spring Embedded Layout on a network.
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param m_anticollisionSpringStrength (string, optional): Strength to apply
to avoid collisions, in numeric value
:param m_averageIterationsPerNode (string, optional): Average number of ite
ratations for each node, in numeric value
:param m_disconnectedNodeDistanceSpringRestLength (string, optional): Rest
length of a 'disconnected' spring, in numeric value
:param m_disconnectedNodeDistanceSpringStrength (string, optional): Strengt
h of a 'disconnected' spring, in numeric value
:param m_layoutPass (string, optional): Number of layout passes, in numeric
value
:param m_nodeDistanceRestLengthConstant (string, optional): Spring rest len
gth, in numeric value
:param m_nodeDistanceStrengthConstant (string, optional): Spring strength,
in numeric value
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param randomize (string, optional): Randomize graph before layout; boolean
values only, true or false; defaults to true
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
:param unweighted (string, optional): Use unweighted edges; boolean values
only, true or false; defaults to false
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['defaultEdgeWeight','EdgeAttribute',\
'm_anticollisionSpringStrength','m_averageIterationsPerNode',\
'm_disconnectedNodeDistanceSpringRestLength',\
'm_disconnectedNodeDistanceSpringStrength','m_layoutPass',\
'm_nodeDistanceRestLengthConstant','m_nodeDistanceStrengthConstant',\
'maxWeightCutoff','minWeightCutoff','network','NodeAttribute','nodeList',\
'randomize','singlePartition','Type','unweighted'],[defaultEdgeWeight,\
EdgeAttribute,m_anticollisionSpringStrength,m_averageIterationsPerNode,\
m_disconnectedNodeDistanceSpringRestLength,\
m_disconnectedNodeDistanceSpringStrength,m_layoutPass,\
m_nodeDistanceRestLengthConstant,m_nodeDistanceStrengthConstant,\
maxWeightCutoff,minWeightCutoff,network,NodeAttribute,nodeList,randomize,\
singlePartition,Type,unweighted])
response=api(url=self.__url+"/kamada-kawai", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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] |
Execute the Edge-weighted Spring Embedded Layout on a network.
:param defaultEdgeWeight (string, optional): The default edge weight to con
sider, default is 0.5
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param m_anticollisionSpringStrength (string, optional): Strength to apply
to avoid collisions, in numeric value
:param m_averageIterationsPerNode (string, optional): Average number of ite
ratations for each node, in numeric value
:param m_disconnectedNodeDistanceSpringRestLength (string, optional): Rest
length of a 'disconnected' spring, in numeric value
:param m_disconnectedNodeDistanceSpringStrength (string, optional): Strengt
h of a 'disconnected' spring, in numeric value
:param m_layoutPass (string, optional): Number of layout passes, in numeric
value
:param m_nodeDistanceRestLengthConstant (string, optional): Spring rest len
gth, in numeric value
:param m_nodeDistanceStrengthConstant (string, optional): Spring strength,
in numeric value
:param maxWeightCutoff (string, optional): The maximum edge weight to consi
der, default to the Double.MAX value
:param minWeightCutoff (string, optional): The minimum edge weight to consi
der, numeric values, default is 0
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param randomize (string, optional): Randomize graph before layout; boolean
values only, true or false; defaults to true
:param singlePartition (string, optional): Don't partition graph before lay
out; boolean values only, true or false; defaults to false
:param Type (string, optional): How to interpret weight values; must be one
of Heuristic, -Log(value), 1 - normalized value and normalized valu
e. Defaults to Heuristic = ['Heuristic', '-Log(value)', '1 - normali
zed value', 'normalized value']
:param unweighted (string, optional): Use unweighted edges; boolean values
only, true or false; defaults to false
|
[
"Execute",
"the",
"Edge",
"-",
"weighted",
"Spring",
"Embedded",
"Layout",
"on",
"a",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L653-L726
|
12,054
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.set_preferred
|
def set_preferred(self,preferredLayout=None,verbose=None):
"""
Sets the preferred layout. Takes a specific name as defined in the API
Default is grid.
:param preferredLayout (string, optional): Layout to use as preferred, for
allowed names see Layout API
"""
PARAMS=set_param(['preferredLayout'],[preferredLayout])
response=api(url=self.__url+"/set preferred", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def set_preferred(self,preferredLayout=None,verbose=None):
"""
Sets the preferred layout. Takes a specific name as defined in the API
Default is grid.
:param preferredLayout (string, optional): Layout to use as preferred, for
allowed names see Layout API
"""
PARAMS=set_param(['preferredLayout'],[preferredLayout])
response=api(url=self.__url+"/set preferred", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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"self",
",",
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",",
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] |
Sets the preferred layout. Takes a specific name as defined in the API
Default is grid.
:param preferredLayout (string, optional): Layout to use as preferred, for
allowed names see Layout API
|
[
"Sets",
"the",
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".",
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"specific",
"name",
"as",
"defined",
"in",
"the",
"API",
"Default",
"is",
"grid",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L729-L739
|
12,055
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/layout.py
|
layout.stacked_node_layout
|
def stacked_node_layout(self,EdgeAttribute=None,network=None,NodeAttribute=None,\
nodeList=None,x_position=None,y_start_position=None,verbose=None):
"""
Execute the Stacked Node Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param x_position (string, optional): X start position, in numeric value
:param y_start_position (string, optional): Y start position, in numeric va
lue
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['EdgeAttribute','network','NodeAttribute','nodeList',\
'x_position','y_start_position'],[EdgeAttribute,network,NodeAttribute,\
nodeList,x_position,y_start_position])
response=api(url=self.__url+"/stacked-node-layout", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def stacked_node_layout(self,EdgeAttribute=None,network=None,NodeAttribute=None,\
nodeList=None,x_position=None,y_start_position=None,verbose=None):
"""
Execute the Stacked Node Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param x_position (string, optional): X start position, in numeric value
:param y_start_position (string, optional): Y start position, in numeric va
lue
"""
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(['EdgeAttribute','network','NodeAttribute','nodeList',\
'x_position','y_start_position'],[EdgeAttribute,network,NodeAttribute,\
nodeList,x_position,y_start_position])
response=api(url=self.__url+"/stacked-node-layout", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Execute the Stacked Node Layout on a network.
:param EdgeAttribute (string, optional): The name of the edge column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param network (string, optional): Specifies a network by name, or by SUID
if the prefix SUID: is used. The keyword CURRENT, or a blank value c
an also be used to specify the current network.
:param NodeAttribute (string, optional): The name of the node column contai
ning numeric values that will be used as weights in the layout algor
ithm. Only columns containing numeric values are shown
:param nodeList (string, optional): Specifies a list of nodes. The keywords
all, selected, or unselected can be used to specify nodes by their
selection state. The pattern COLUMN:VALUE sets this parameter to any
rows that contain the specified column value; if the COLUMN prefix
is not used, the NAME column is matched by default. A list of COLUMN
:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be
used to match multiple values.
:param x_position (string, optional): X start position, in numeric value
:param y_start_position (string, optional): Y start position, in numeric va
lue
|
[
"Execute",
"the",
"Stacked",
"Node",
"Layout",
"on",
"a",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/layout.py#L742-L772
|
12,056
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.create_column
|
def create_column(self,columnName=None,listType=None,table=None,ntype=None,verbose=None):
"""
Appends an additional column of attribute values to the current table.
:param columnName (string, optional): The new column name
:param listType (string, optional): Can be one of integer, long, double, or
string.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param ntype (string, optional): Can be one of integer, long, double, string
, or list.
"""
PARAMS=set_param(['columnName','listType','table','type'],[columnName,\
listType,table,ntype])
response=api(url=self.__url+"/create column", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def create_column(self,columnName=None,listType=None,table=None,ntype=None,verbose=None):
"""
Appends an additional column of attribute values to the current table.
:param columnName (string, optional): The new column name
:param listType (string, optional): Can be one of integer, long, double, or
string.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param ntype (string, optional): Can be one of integer, long, double, string
, or list.
"""
PARAMS=set_param(['columnName','listType','table','type'],[columnName,\
listType,table,ntype])
response=api(url=self.__url+"/create column", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Appends an additional column of attribute values to the current table.
:param columnName (string, optional): The new column name
:param listType (string, optional): Can be one of integer, long, double, or
string.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param ntype (string, optional): Can be one of integer, long, double, string
, or list.
|
[
"Appends",
"an",
"additional",
"column",
"of",
"attribute",
"values",
"to",
"the",
"current",
"table",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L30-L46
|
12,057
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.create_table
|
def create_table(self,keyColumn=None,keyColumnType=None,title=None,verbose=None):
"""
Adds a new table to the network.
:param keyColumn (string, optional): Specifies the name of a column in the
table
:param keyColumnType (string, optional): The syntactical type of the value
used in the key
:param title (string, optional): The name of the table used in the current
network
:returns: table SUID
"""
PARAMS=set_param(['keyColumn','keyColumnType','title'],[keyColumn,\
keyColumnType,title])
response=api(url=self.__url+"/create table", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def create_table(self,keyColumn=None,keyColumnType=None,title=None,verbose=None):
"""
Adds a new table to the network.
:param keyColumn (string, optional): Specifies the name of a column in the
table
:param keyColumnType (string, optional): The syntactical type of the value
used in the key
:param title (string, optional): The name of the table used in the current
network
:returns: table SUID
"""
PARAMS=set_param(['keyColumn','keyColumnType','title'],[keyColumn,\
keyColumnType,title])
response=api(url=self.__url+"/create table", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
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] |
Adds a new table to the network.
:param keyColumn (string, optional): Specifies the name of a column in the
table
:param keyColumnType (string, optional): The syntactical type of the value
used in the key
:param title (string, optional): The name of the table used in the current
network
:returns: table SUID
|
[
"Adds",
"a",
"new",
"table",
"to",
"the",
"network",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L49-L65
|
12,058
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.delete_column
|
def delete_column(self,column=None,table=None,verbose=None):
"""
Remove a column from a table, specified by its name. Returns the name of
the column removed.
:param column (string, optional): Specifies the name of a column in the tab
le
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
"""
PARAMS=set_param(['column','table'],[column,table])
response=api(url=self.__url+"/delete column", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def delete_column(self,column=None,table=None,verbose=None):
"""
Remove a column from a table, specified by its name. Returns the name of
the column removed.
:param column (string, optional): Specifies the name of a column in the tab
le
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
"""
PARAMS=set_param(['column','table'],[column,table])
response=api(url=self.__url+"/delete column", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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Remove a column from a table, specified by its name. Returns the name of
the column removed.
:param column (string, optional): Specifies the name of a column in the tab
le
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
|
[
"Remove",
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"name",
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"Returns",
"the",
"name",
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"the",
"column",
"removed",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L67-L80
|
12,059
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.delete_row
|
def delete_row(self,keyValue=None,table=None,verbose=None):
"""
Deletes a row from a table.Requires the table name or SUID and the row key.
:param keyValue (string): Specifies the primary key of a value in the row o
f a table
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
"""
PARAMS=set_param(['keyValue','table'],[keyValue,table])
response=api(url=self.__url+"/delete row", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def delete_row(self,keyValue=None,table=None,verbose=None):
"""
Deletes a row from a table.Requires the table name or SUID and the row key.
:param keyValue (string): Specifies the primary key of a value in the row o
f a table
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
"""
PARAMS=set_param(['keyValue','table'],[keyValue,table])
response=api(url=self.__url+"/delete row", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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Deletes a row from a table.Requires the table name or SUID and the row key.
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f a table
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
|
[
"Deletes",
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"Requires",
"the",
"table",
"name",
"or",
"SUID",
"and",
"the",
"row",
"key",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L83-L95
|
12,060
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.get_value
|
def get_value(self,column=None,keyValue=None,table=None,verbose=None):
"""
Returns the value from a cell as specified by row and column ids.
:param column (string, optional): Specifies the name of a column in the tab
le
:param keyValue (string, optional): Specifies a row of a table using the pr
imary key as the indentifier
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:returns: value from a cell as specified by row and column ids
"""
PARAMS=set_param(['column','keyValue','table'],[column,keyValue,table])
response=api(url=self.__url+"/get value", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def get_value(self,column=None,keyValue=None,table=None,verbose=None):
"""
Returns the value from a cell as specified by row and column ids.
:param column (string, optional): Specifies the name of a column in the tab
le
:param keyValue (string, optional): Specifies a row of a table using the pr
imary key as the indentifier
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:returns: value from a cell as specified by row and column ids
"""
PARAMS=set_param(['column','keyValue','table'],[column,keyValue,table])
response=api(url=self.__url+"/get value", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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Returns the value from a cell as specified by row and column ids.
:param column (string, optional): Specifies the name of a column in the tab
le
:param keyValue (string, optional): Specifies a row of a table using the pr
imary key as the indentifier
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:returns: value from a cell as specified by row and column ids
|
[
"Returns",
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"from",
"a",
"cell",
"as",
"specified",
"by",
"row",
"and",
"column",
"ids",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L160-L176
|
12,061
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.import_url
|
def import_url(self,caseSensitiveNetworkCollectionKeys=None,\
caseSensitiveNetworkKeys=None,dataTypeList=None,\
DataTypeTargetForNetworkCollection=None,DataTypeTargetForNetworkList=None,\
delimiters=None,delimitersForDataList=None,firstRowAsColumnNames=None,\
KeyColumnForMapping=None,KeyColumnForMappingNetworkList=None,\
keyColumnIndex=None,newTableName=None,startLoadRow=None,\
TargetNetworkCollection=None,TargetNetworkList=None,url=None,\
WhereImportTable=None,verbose=None):
"""
Similar to Import Table this uses a long list of input parameters to
specify the attributes of the table, the mapping keys, and the destination
table for the input.
:param caseSensitiveNetworkCollectionKeys (string, optional): Determines wh
ether capitalization is considered in matching and sorting
:param caseSensitiveNetworkKeys (string, optional): Determines whether capi
talization is considered in matching and sorting
:param dataTypeList (string, optional): List of column data types ordered b
y column index (e.g. "string,int,long,double,boolean,intlist" or jus
t "s,i,l,d,b,il")
:param DataTypeTargetForNetworkCollection (string, optional): Select whethe
r to import the data as Node Table Columns, Edge Table Columns, or N
etwork Table Columns
:param DataTypeTargetForNetworkList (string, optional): The data type of th
e targets
:param delimiters (string, optional): The list of delimiters that separate
columns in the table.
:param delimitersForDataList (string, optional): The delimiters between ele
ments of list columns in the table.
:param firstRowAsColumnNames (string, optional): If the first imported row
contains column names, set this to true.
:param KeyColumnForMapping (string, optional): The column in the network to
use as the merge key
:param KeyColumnForMappingNetworkList (string, optional): The column in the
network to use as the merge key
:param keyColumnIndex (string, optional): The column that contains the key
values for this import. These values will be used to match with the
key values in the network.
:param newTableName (string, optional): The title of the new table
:param startLoadRow (string, optional): The first row of the input table to
load. This allows the skipping of headers that are not part of the
import.
:param TargetNetworkCollection (string, optional): The network collection t
o use for the table import
:param TargetNetworkList (string, optional): The list of networks into whic
h the table is imported
:param url (string): The URL of the file or resource that provides the tabl
e or network to be imported.
:param WhereImportTable (string, optional): Determines what network(s) the
imported table will be associated with (if any). A table can be impo
rted into a Network Collection, Selected networks or to an unassigne
d table.
"""
PARAMS=set_param(['caseSensitiveNetworkCollectionKeys',\
'caseSensitiveNetworkKeys','dataTypeList','DataTypeTargetForNetworkCollection',\
'DataTypeTargetForNetworkList','delimiters','delimitersForDataList',\
'firstRowAsColumnNames','KeyColumnForMapping','KeyColumnForMappingNetworkList',\
'keyColumnIndex','newTableName','startLoadRow','TargetNetworkCollection',\
'TargetNetworkList','url','WhereImportTable'],[caseSensitiveNetworkCollectionKeys,\
caseSensitiveNetworkKeys,dataTypeList,DataTypeTargetForNetworkCollection,\
DataTypeTargetForNetworkList,delimiters,delimitersForDataList,\
firstRowAsColumnNames,KeyColumnForMapping,KeyColumnForMappingNetworkList,\
keyColumnIndex,newTableName,startLoadRow,TargetNetworkCollection,\
TargetNetworkList,url,WhereImportTable])
response=api(url=self.__url+"/import url", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def import_url(self,caseSensitiveNetworkCollectionKeys=None,\
caseSensitiveNetworkKeys=None,dataTypeList=None,\
DataTypeTargetForNetworkCollection=None,DataTypeTargetForNetworkList=None,\
delimiters=None,delimitersForDataList=None,firstRowAsColumnNames=None,\
KeyColumnForMapping=None,KeyColumnForMappingNetworkList=None,\
keyColumnIndex=None,newTableName=None,startLoadRow=None,\
TargetNetworkCollection=None,TargetNetworkList=None,url=None,\
WhereImportTable=None,verbose=None):
"""
Similar to Import Table this uses a long list of input parameters to
specify the attributes of the table, the mapping keys, and the destination
table for the input.
:param caseSensitiveNetworkCollectionKeys (string, optional): Determines wh
ether capitalization is considered in matching and sorting
:param caseSensitiveNetworkKeys (string, optional): Determines whether capi
talization is considered in matching and sorting
:param dataTypeList (string, optional): List of column data types ordered b
y column index (e.g. "string,int,long,double,boolean,intlist" or jus
t "s,i,l,d,b,il")
:param DataTypeTargetForNetworkCollection (string, optional): Select whethe
r to import the data as Node Table Columns, Edge Table Columns, or N
etwork Table Columns
:param DataTypeTargetForNetworkList (string, optional): The data type of th
e targets
:param delimiters (string, optional): The list of delimiters that separate
columns in the table.
:param delimitersForDataList (string, optional): The delimiters between ele
ments of list columns in the table.
:param firstRowAsColumnNames (string, optional): If the first imported row
contains column names, set this to true.
:param KeyColumnForMapping (string, optional): The column in the network to
use as the merge key
:param KeyColumnForMappingNetworkList (string, optional): The column in the
network to use as the merge key
:param keyColumnIndex (string, optional): The column that contains the key
values for this import. These values will be used to match with the
key values in the network.
:param newTableName (string, optional): The title of the new table
:param startLoadRow (string, optional): The first row of the input table to
load. This allows the skipping of headers that are not part of the
import.
:param TargetNetworkCollection (string, optional): The network collection t
o use for the table import
:param TargetNetworkList (string, optional): The list of networks into whic
h the table is imported
:param url (string): The URL of the file or resource that provides the tabl
e or network to be imported.
:param WhereImportTable (string, optional): Determines what network(s) the
imported table will be associated with (if any). A table can be impo
rted into a Network Collection, Selected networks or to an unassigne
d table.
"""
PARAMS=set_param(['caseSensitiveNetworkCollectionKeys',\
'caseSensitiveNetworkKeys','dataTypeList','DataTypeTargetForNetworkCollection',\
'DataTypeTargetForNetworkList','delimiters','delimitersForDataList',\
'firstRowAsColumnNames','KeyColumnForMapping','KeyColumnForMappingNetworkList',\
'keyColumnIndex','newTableName','startLoadRow','TargetNetworkCollection',\
'TargetNetworkList','url','WhereImportTable'],[caseSensitiveNetworkCollectionKeys,\
caseSensitiveNetworkKeys,dataTypeList,DataTypeTargetForNetworkCollection,\
DataTypeTargetForNetworkList,delimiters,delimitersForDataList,\
firstRowAsColumnNames,KeyColumnForMapping,KeyColumnForMappingNetworkList,\
keyColumnIndex,newTableName,startLoadRow,TargetNetworkCollection,\
TargetNetworkList,url,WhereImportTable])
response=api(url=self.__url+"/import url", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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"verbose",
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] |
Similar to Import Table this uses a long list of input parameters to
specify the attributes of the table, the mapping keys, and the destination
table for the input.
:param caseSensitiveNetworkCollectionKeys (string, optional): Determines wh
ether capitalization is considered in matching and sorting
:param caseSensitiveNetworkKeys (string, optional): Determines whether capi
talization is considered in matching and sorting
:param dataTypeList (string, optional): List of column data types ordered b
y column index (e.g. "string,int,long,double,boolean,intlist" or jus
t "s,i,l,d,b,il")
:param DataTypeTargetForNetworkCollection (string, optional): Select whethe
r to import the data as Node Table Columns, Edge Table Columns, or N
etwork Table Columns
:param DataTypeTargetForNetworkList (string, optional): The data type of th
e targets
:param delimiters (string, optional): The list of delimiters that separate
columns in the table.
:param delimitersForDataList (string, optional): The delimiters between ele
ments of list columns in the table.
:param firstRowAsColumnNames (string, optional): If the first imported row
contains column names, set this to true.
:param KeyColumnForMapping (string, optional): The column in the network to
use as the merge key
:param KeyColumnForMappingNetworkList (string, optional): The column in the
network to use as the merge key
:param keyColumnIndex (string, optional): The column that contains the key
values for this import. These values will be used to match with the
key values in the network.
:param newTableName (string, optional): The title of the new table
:param startLoadRow (string, optional): The first row of the input table to
load. This allows the skipping of headers that are not part of the
import.
:param TargetNetworkCollection (string, optional): The network collection t
o use for the table import
:param TargetNetworkList (string, optional): The list of networks into whic
h the table is imported
:param url (string): The URL of the file or resource that provides the tabl
e or network to be imported.
:param WhereImportTable (string, optional): Determines what network(s) the
imported table will be associated with (if any). A table can be impo
rted into a Network Collection, Selected networks or to an unassigne
d table.
|
[
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"keys",
"and",
"the",
"destination",
"table",
"for",
"the",
"input",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L246-L311
|
12,062
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.list_tables
|
def list_tables(self,includePrivate=None,namespace=None,atype=None,verbose=None):
"""
Returns a list of the table SUIDs associated with the passed network parameter.
:param includePrivate (string, optional): A boolean value determining wheth
er to return private as well as public tables
:param namespace (string, optional): An optional argument to contrain outpu
t to a single namespace, or ALL
:param atype (string, optional): One of ''network'', ''node'', ''edge'', ''u
nattached'', ''all'', to constrain the type of table listed
:returns: list of the table SUIDs associated with the passed network parameter.
"""
PARAMS=set_param(['includePrivate','namespace','type'],\
[includePrivate,namespace,atype])
response=api(url=self.__url+"/list", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def list_tables(self,includePrivate=None,namespace=None,atype=None,verbose=None):
"""
Returns a list of the table SUIDs associated with the passed network parameter.
:param includePrivate (string, optional): A boolean value determining wheth
er to return private as well as public tables
:param namespace (string, optional): An optional argument to contrain outpu
t to a single namespace, or ALL
:param atype (string, optional): One of ''network'', ''node'', ''edge'', ''u
nattached'', ''all'', to constrain the type of table listed
:returns: list of the table SUIDs associated with the passed network parameter.
"""
PARAMS=set_param(['includePrivate','namespace','type'],\
[includePrivate,namespace,atype])
response=api(url=self.__url+"/list", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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] |
Returns a list of the table SUIDs associated with the passed network parameter.
:param includePrivate (string, optional): A boolean value determining wheth
er to return private as well as public tables
:param namespace (string, optional): An optional argument to contrain outpu
t to a single namespace, or ALL
:param atype (string, optional): One of ''network'', ''node'', ''edge'', ''u
nattached'', ''all'', to constrain the type of table listed
:returns: list of the table SUIDs associated with the passed network parameter.
|
[
"Returns",
"a",
"list",
"of",
"the",
"table",
"SUIDs",
"associated",
"with",
"the",
"passed",
"network",
"parameter",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L314-L329
|
12,063
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.list_columns
|
def list_columns(self,table=None,verbose=None):
"""
Returns the list of columns in the table.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:returns: list of columns in the table.
"""
PARAMS=set_param(['table'],[table])
response=api(url=self.__url+"/list columns", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def list_columns(self,table=None,verbose=None):
"""
Returns the list of columns in the table.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:returns: list of columns in the table.
"""
PARAMS=set_param(['table'],[table])
response=api(url=self.__url+"/list columns", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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] |
Returns the list of columns in the table.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:returns: list of columns in the table.
|
[
"Returns",
"the",
"list",
"of",
"columns",
"in",
"the",
"table",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L332-L343
|
12,064
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.list_rows
|
def list_rows(self,rowList=None,table=None,verbose=None):
"""
Returns the list of primary keys for each of the rows in the specified table.
:param rowList (string, optional): Specifies a list of rows. The pattern CO
LUMN:VALUE sets this parameter to any rows that contain the specifie
d column value; if the COLUMN prefix is not used, the NAME column is
matched by default. A list of COLUMN:VALUE pairs of the format COLU
MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.
This parameter can also be set to all to include all rows.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
"""
PARAMS=set_param(['rowList','table'],[rowList,table])
response=api(url=self.__url+"/list rows", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def list_rows(self,rowList=None,table=None,verbose=None):
"""
Returns the list of primary keys for each of the rows in the specified table.
:param rowList (string, optional): Specifies a list of rows. The pattern CO
LUMN:VALUE sets this parameter to any rows that contain the specifie
d column value; if the COLUMN prefix is not used, the NAME column is
matched by default. A list of COLUMN:VALUE pairs of the format COLU
MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.
This parameter can also be set to all to include all rows.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
"""
PARAMS=set_param(['rowList','table'],[rowList,table])
response=api(url=self.__url+"/list rows", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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"=",
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"verbose",
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] |
Returns the list of primary keys for each of the rows in the specified table.
:param rowList (string, optional): Specifies a list of rows. The pattern CO
LUMN:VALUE sets this parameter to any rows that contain the specifie
d column value; if the COLUMN prefix is not used, the NAME column is
matched by default. A list of COLUMN:VALUE pairs of the format COLU
MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.
This parameter can also be set to all to include all rows.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
|
[
"Returns",
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"keys",
"for",
"each",
"of",
"the",
"rows",
"in",
"the",
"specified",
"table",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L346-L362
|
12,065
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.merge
|
def merge(self,DataTypeTargetForNetworkCollection=None,\
dataTypeTargetForNetworkList=None,mergeType=None,SourceMergeColumns=None,\
SourceMergeKey=None,SourceTable=None,TargetKeyNetworkCollection=None,\
TargetMergeKey=None,TargetNetworkCollection=None,TargetNetworkList=None,\
UnassignedTable=None,WhereMergeTable=None,verbose=None):
"""
Merge tables together joining around a designated key column. Depending
on the arguments, might merge into multiple local tables.
:param DataTypeTargetForNetworkCollection (string, optional): The collectio
n of networks where the merged table will reside
:param dataTypeTargetForNetworkList (string, optional):
:param mergeType (string, optional): A choice between ''Copy Columns'' and
''Link To Columns'' that determines if replicates are created
:param SourceMergeColumns (string, optional): A list of columns that will b
e brought into the merged table
:param SourceMergeKey (string, optional): The name of the columns that exis
ts in both tables and is used to correlate rows
:param SourceTable (string, optional): The name of the table used as the ba
se data in the merge
:param TargetKeyNetworkCollection (string, optional): The name of the prima
ry column about which the merge is made
:param TargetMergeKey (string, optional):
:param TargetNetworkCollection (string, optional): The group of networks th
at will be merged into the source table
:param TargetNetworkList (string, optional): The list of networks where the
merged table will be added
:param UnassignedTable (string, optional):
:param WhereMergeTable (string, optional): The destination path of the resu
ltant merged table. The choices are ''Network Collection'', ''Select
ed Networks'', or ''All Unassigned Tables''.
"""
PARAMS=set_param(['DataTypeTargetForNetworkCollection','dataTypeTargetForNetworkList','mergeType','SourceMergeColumns','SourceMergeKey','SourceTable','TargetKeyNetworkCollection','TargetMergeKey','TargetNetworkCollection','TargetNetworkList','UnassignedTable','WhereMergeTable'],\
[DataTypeTargetForNetworkCollection,dataTypeTargetForNetworkList,mergeType,SourceMergeColumns,SourceMergeKey,SourceTable,TargetKeyNetworkCollection,TargetMergeKey,TargetNetworkCollection,TargetNetworkList,UnassignedTable,WhereMergeTable])
response=api(url=self.__url+"/merge", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def merge(self,DataTypeTargetForNetworkCollection=None,\
dataTypeTargetForNetworkList=None,mergeType=None,SourceMergeColumns=None,\
SourceMergeKey=None,SourceTable=None,TargetKeyNetworkCollection=None,\
TargetMergeKey=None,TargetNetworkCollection=None,TargetNetworkList=None,\
UnassignedTable=None,WhereMergeTable=None,verbose=None):
"""
Merge tables together joining around a designated key column. Depending
on the arguments, might merge into multiple local tables.
:param DataTypeTargetForNetworkCollection (string, optional): The collectio
n of networks where the merged table will reside
:param dataTypeTargetForNetworkList (string, optional):
:param mergeType (string, optional): A choice between ''Copy Columns'' and
''Link To Columns'' that determines if replicates are created
:param SourceMergeColumns (string, optional): A list of columns that will b
e brought into the merged table
:param SourceMergeKey (string, optional): The name of the columns that exis
ts in both tables and is used to correlate rows
:param SourceTable (string, optional): The name of the table used as the ba
se data in the merge
:param TargetKeyNetworkCollection (string, optional): The name of the prima
ry column about which the merge is made
:param TargetMergeKey (string, optional):
:param TargetNetworkCollection (string, optional): The group of networks th
at will be merged into the source table
:param TargetNetworkList (string, optional): The list of networks where the
merged table will be added
:param UnassignedTable (string, optional):
:param WhereMergeTable (string, optional): The destination path of the resu
ltant merged table. The choices are ''Network Collection'', ''Select
ed Networks'', or ''All Unassigned Tables''.
"""
PARAMS=set_param(['DataTypeTargetForNetworkCollection','dataTypeTargetForNetworkList','mergeType','SourceMergeColumns','SourceMergeKey','SourceTable','TargetKeyNetworkCollection','TargetMergeKey','TargetNetworkCollection','TargetNetworkList','UnassignedTable','WhereMergeTable'],\
[DataTypeTargetForNetworkCollection,dataTypeTargetForNetworkList,mergeType,SourceMergeColumns,SourceMergeKey,SourceTable,TargetKeyNetworkCollection,TargetMergeKey,TargetNetworkCollection,TargetNetworkList,UnassignedTable,WhereMergeTable])
response=api(url=self.__url+"/merge", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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",",
"SourceMergeKey",
",",
"SourceTable",
",",
"TargetKeyNetworkCollection",
",",
"TargetMergeKey",
",",
"TargetNetworkCollection",
",",
"TargetNetworkList",
",",
"UnassignedTable",
",",
"WhereMergeTable",
"]",
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"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Merge tables together joining around a designated key column. Depending
on the arguments, might merge into multiple local tables.
:param DataTypeTargetForNetworkCollection (string, optional): The collectio
n of networks where the merged table will reside
:param dataTypeTargetForNetworkList (string, optional):
:param mergeType (string, optional): A choice between ''Copy Columns'' and
''Link To Columns'' that determines if replicates are created
:param SourceMergeColumns (string, optional): A list of columns that will b
e brought into the merged table
:param SourceMergeKey (string, optional): The name of the columns that exis
ts in both tables and is used to correlate rows
:param SourceTable (string, optional): The name of the table used as the ba
se data in the merge
:param TargetKeyNetworkCollection (string, optional): The name of the prima
ry column about which the merge is made
:param TargetMergeKey (string, optional):
:param TargetNetworkCollection (string, optional): The group of networks th
at will be merged into the source table
:param TargetNetworkList (string, optional): The list of networks where the
merged table will be added
:param UnassignedTable (string, optional):
:param WhereMergeTable (string, optional): The destination path of the resu
ltant merged table. The choices are ''Network Collection'', ''Select
ed Networks'', or ''All Unassigned Tables''.
|
[
"Merge",
"tables",
"together",
"joining",
"around",
"a",
"designated",
"key",
"column",
".",
"Depending",
"on",
"the",
"arguments",
"might",
"merge",
"into",
"multiple",
"local",
"tables",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L365-L400
|
12,066
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.rename_column
|
def rename_column(self,columnName=None,newColumnName=None,table=None,verbose=None):
"""
Changes the name of a specified column in the table.
:param columnName (string): The name of the column that will be renamed.
:param newColumnName (string): The new name of the column.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
"""
PARAMS=set_param(['columnName','newColumnName','table'],[columnName,newColumnName,table])
response=api(url=self.__url+"/rename column", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def rename_column(self,columnName=None,newColumnName=None,table=None,verbose=None):
"""
Changes the name of a specified column in the table.
:param columnName (string): The name of the column that will be renamed.
:param newColumnName (string): The new name of the column.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
"""
PARAMS=set_param(['columnName','newColumnName','table'],[columnName,newColumnName,table])
response=api(url=self.__url+"/rename column", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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"method",
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"verbose",
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"return",
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] |
Changes the name of a specified column in the table.
:param columnName (string): The name of the column that will be renamed.
:param newColumnName (string): The new name of the column.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
|
[
"Changes",
"the",
"name",
"of",
"a",
"specified",
"column",
"in",
"the",
"table",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L404-L416
|
12,067
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.set_title
|
def set_title(self,table=None,title=None,verbose=None):
"""
Changes the visible identifier of a single table.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param title (string, optional): The name of the table used in the current
network
"""
PARAMS=set_param(['table','title'],[table,title])
response=api(url=self.__url+"/set title", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def set_title(self,table=None,title=None,verbose=None):
"""
Changes the visible identifier of a single table.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param title (string, optional): The name of the table used in the current
network
"""
PARAMS=set_param(['table','title'],[table,title])
response=api(url=self.__url+"/set title", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
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Changes the visible identifier of a single table.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param title (string, optional): The name of the table used in the current
network
|
[
"Changes",
"the",
"visible",
"identifier",
"of",
"a",
"single",
"table",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L420-L432
|
12,068
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.set_values
|
def set_values(self,columnName=None,rowList=None,table=None,value=None,verbose=None):
"""
Set all the values in the specified list of rows with a single value.
:param columnName (string, optional): Specifies the name of a column in the
table
:param rowList (string, optional): Specifies a list of rows. The pattern CO
LUMN:VALUE sets this parameter to any rows that contain the specifie
d column value; if the COLUMN prefix is not used, the NAME column is
matched by default. A list of COLUMN:VALUE pairs of the format COLU
MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.
This parameter can also be set to all to include all rows.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param value (string, optional): The value to set the columns in the select
ed rows to. This should be a string value, which will be converted t
o the appropriate column type.
"""
PARAMS=set_param(['columnName','rowList','table','value'],[columnName,rowList,table,value])
response=api(url=self.__url+"/set values", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def set_values(self,columnName=None,rowList=None,table=None,value=None,verbose=None):
"""
Set all the values in the specified list of rows with a single value.
:param columnName (string, optional): Specifies the name of a column in the
table
:param rowList (string, optional): Specifies a list of rows. The pattern CO
LUMN:VALUE sets this parameter to any rows that contain the specifie
d column value; if the COLUMN prefix is not used, the NAME column is
matched by default. A list of COLUMN:VALUE pairs of the format COLU
MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.
This parameter can also be set to all to include all rows.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param value (string, optional): The value to set the columns in the select
ed rows to. This should be a string value, which will be converted t
o the appropriate column type.
"""
PARAMS=set_param(['columnName','rowList','table','value'],[columnName,rowList,table,value])
response=api(url=self.__url+"/set values", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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"\"POST\"",
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"verbose",
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"verbose",
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] |
Set all the values in the specified list of rows with a single value.
:param columnName (string, optional): Specifies the name of a column in the
table
:param rowList (string, optional): Specifies a list of rows. The pattern CO
LUMN:VALUE sets this parameter to any rows that contain the specifie
d column value; if the COLUMN prefix is not used, the NAME column is
matched by default. A list of COLUMN:VALUE pairs of the format COLU
MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.
This parameter can also be set to all to include all rows.
:param table (string, optional): Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
:param value (string, optional): The value to set the columns in the select
ed rows to. This should be a string value, which will be converted t
o the appropriate column type.
|
[
"Set",
"all",
"the",
"values",
"in",
"the",
"specified",
"list",
"of",
"rows",
"with",
"a",
"single",
"value",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L436-L457
|
12,069
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.getTable
|
def getTable(self, columns=None, table=None, network = "current", namespace='default', verbose=VERBOSE):
"""
Gets tables from cytoscape.
:param table: table to retrieve eg. node
:param columns: columns to retrieve in list format
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param namespace (string, optional): Node, Edge, and Network objects support
the default, local, and hidden namespaces. Root networks also support the
shared namespace. Custom namespaces may be specified by Apps.
:returns: a pandas dataframe
"""
u=self.__url
host=u.split("//")[1].split(":")[0]
port=u.split(":")[2].split("/")[0]
version=u.split(":")[2].split("/")[1]
if type(network) != int:
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["columnList","namespace","network"],["SUID",namespace,network])
network=api(namespace="network", command="get attribute",PARAMS=PARAMS, host=host,port=str(port),version=version)
network=network[0]["SUID"]
df=pd.DataFrame()
def target(column):
URL="http://"+str(host)+":"+str(port)+"/v1/networks/"+str(network)+"/tables/"+namespace+table+"/columns/"+column
if verbose:
print("'"+URL+"'")
sys.stdout.flush()
response = urllib2.urlopen(URL)
response = response.read()
colA=json.loads(response)
col=pd.DataFrame()
colHeader=colA["name"]
colValues=colA["values"]
col[colHeader]=colValues
return col
ncols=["name"]
for c in columns:
ncols.append(c.replace(" ","%20") )
for c in ncols:
try:
col=target(c)
df=pd.concat([df,col],axis=1)
except:
print("Could not find "+c)
sys.stdout.flush()
df.index=df["name"].tolist()
df=df.drop(["name"],axis=1)
return df
|
python
|
def getTable(self, columns=None, table=None, network = "current", namespace='default', verbose=VERBOSE):
"""
Gets tables from cytoscape.
:param table: table to retrieve eg. node
:param columns: columns to retrieve in list format
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param namespace (string, optional): Node, Edge, and Network objects support
the default, local, and hidden namespaces. Root networks also support the
shared namespace. Custom namespaces may be specified by Apps.
:returns: a pandas dataframe
"""
u=self.__url
host=u.split("//")[1].split(":")[0]
port=u.split(":")[2].split("/")[0]
version=u.split(":")[2].split("/")[1]
if type(network) != int:
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["columnList","namespace","network"],["SUID",namespace,network])
network=api(namespace="network", command="get attribute",PARAMS=PARAMS, host=host,port=str(port),version=version)
network=network[0]["SUID"]
df=pd.DataFrame()
def target(column):
URL="http://"+str(host)+":"+str(port)+"/v1/networks/"+str(network)+"/tables/"+namespace+table+"/columns/"+column
if verbose:
print("'"+URL+"'")
sys.stdout.flush()
response = urllib2.urlopen(URL)
response = response.read()
colA=json.loads(response)
col=pd.DataFrame()
colHeader=colA["name"]
colValues=colA["values"]
col[colHeader]=colValues
return col
ncols=["name"]
for c in columns:
ncols.append(c.replace(" ","%20") )
for c in ncols:
try:
col=target(c)
df=pd.concat([df,col],axis=1)
except:
print("Could not find "+c)
sys.stdout.flush()
df.index=df["name"].tolist()
df=df.drop(["name"],axis=1)
return df
|
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] |
Gets tables from cytoscape.
:param table: table to retrieve eg. node
:param columns: columns to retrieve in list format
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param namespace (string, optional): Node, Edge, and Network objects support
the default, local, and hidden namespaces. Root networks also support the
shared namespace. Custom namespaces may be specified by Apps.
:returns: a pandas dataframe
|
[
"Gets",
"tables",
"from",
"cytoscape",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L459-L515
|
12,070
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.loadTableData
|
def loadTableData(self, df, df_key='index',table="node", table_key_column = "name", \
network="current",namespace="default",verbose=False):
"""
Loads tables into cytoscape.
:param df: a pandas dataframe to load
:param df_key: key column in df, default="index"
:param table: target table, default="node"
:param table_key_column: table key column, default="name"
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param namespace (string, optional): Node, Edge, and Network objects support
the default, local, and hidden namespaces. Root networks also support the
shared namespace. Custom namespaces may be specified by Apps.
:param verbose: print more information
:returns: output of put request
"""
u=self.__url
host=u.split("//")[1].split(":")[0]
port=u.split(":")[2].split("/")[0]
version=u.split(":")[2].split("/")[1]
if type(network) != int:
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["columnList","namespace","network"],["SUID",namespace,network])
networkID=api(namespace="network", command="get attribute",PARAMS=PARAMS, host=host,port=str(port),version=version)
PARAMS=set_param(["columnList","namespace","network"],["name",namespace,network])
networkname=api(namespace="network", command="get attribute",PARAMS=PARAMS, host=host,port=str(port),version=version)
network=networkID[0]["SUID"]
networkname=networkname[0]["name"]
tmp=df.copy()
if df_key!="index":
tmp.index=tmp[df_key].tolist()
tmp=tmp.drop([df_key],axis=1)
tablen=networkname+" default node"
data=[]
for c in tmp.columns.tolist():
tmpcol=tmp[[c]].dropna()
for r in tmpcol.index.tolist():
cell={}
cell[str(table_key_column)]=str(r) # {"name":"p53"}
val=tmpcol.loc[r,c]
if type(val) != str:
val=float(val)
cell[str(c)]=val
data.append(cell)
upload={"key":table_key_column,"dataKey":table_key_column,\
"data":data}
URL="http://"+str(host)+":"+str(port)+"/v1/networks/"+str(network)+"/tables/"+namespace+table
if verbose:
print("'"+URL+"'", upload)
sys.stdout.flush()
r = requests.put(url = URL, json = upload)
if verbose:
print(r)
checkresponse(r)
res=r.content
return res
|
python
|
def loadTableData(self, df, df_key='index',table="node", table_key_column = "name", \
network="current",namespace="default",verbose=False):
"""
Loads tables into cytoscape.
:param df: a pandas dataframe to load
:param df_key: key column in df, default="index"
:param table: target table, default="node"
:param table_key_column: table key column, default="name"
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param namespace (string, optional): Node, Edge, and Network objects support
the default, local, and hidden namespaces. Root networks also support the
shared namespace. Custom namespaces may be specified by Apps.
:param verbose: print more information
:returns: output of put request
"""
u=self.__url
host=u.split("//")[1].split(":")[0]
port=u.split(":")[2].split("/")[0]
version=u.split(":")[2].split("/")[1]
if type(network) != int:
network=check_network(self,network,verbose=verbose)
PARAMS=set_param(["columnList","namespace","network"],["SUID",namespace,network])
networkID=api(namespace="network", command="get attribute",PARAMS=PARAMS, host=host,port=str(port),version=version)
PARAMS=set_param(["columnList","namespace","network"],["name",namespace,network])
networkname=api(namespace="network", command="get attribute",PARAMS=PARAMS, host=host,port=str(port),version=version)
network=networkID[0]["SUID"]
networkname=networkname[0]["name"]
tmp=df.copy()
if df_key!="index":
tmp.index=tmp[df_key].tolist()
tmp=tmp.drop([df_key],axis=1)
tablen=networkname+" default node"
data=[]
for c in tmp.columns.tolist():
tmpcol=tmp[[c]].dropna()
for r in tmpcol.index.tolist():
cell={}
cell[str(table_key_column)]=str(r) # {"name":"p53"}
val=tmpcol.loc[r,c]
if type(val) != str:
val=float(val)
cell[str(c)]=val
data.append(cell)
upload={"key":table_key_column,"dataKey":table_key_column,\
"data":data}
URL="http://"+str(host)+":"+str(port)+"/v1/networks/"+str(network)+"/tables/"+namespace+table
if verbose:
print("'"+URL+"'", upload)
sys.stdout.flush()
r = requests.put(url = URL, json = upload)
if verbose:
print(r)
checkresponse(r)
res=r.content
return res
|
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Loads tables into cytoscape.
:param df: a pandas dataframe to load
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:param table: target table, default="node"
:param table_key_column: table key column, default="name"
:param network (string, optional): Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
:param namespace (string, optional): Node, Edge, and Network objects support
the default, local, and hidden namespaces. Root networks also support the
shared namespace. Custom namespaces may be specified by Apps.
:param verbose: print more information
:returns: output of put request
|
[
"Loads",
"tables",
"into",
"cytoscape",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L517-L588
|
12,071
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/table.py
|
table.getTableCount
|
def getTableCount(verbose=None):
"""
Returns the number of global tables.
:param verbose: print more
:returns: 200: successful operation
"""
response=api(url=self.url+'tables/count', method="GET", verbose=verbose, parse_params=False)
return response
|
python
|
def getTableCount(verbose=None):
"""
Returns the number of global tables.
:param verbose: print more
:returns: 200: successful operation
"""
response=api(url=self.url+'tables/count', method="GET", verbose=verbose, parse_params=False)
return response
|
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Returns the number of global tables.
:param verbose: print more
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|
[
"Returns",
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"global",
"tables",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/table.py#L590-L600
|
12,072
|
cytoscape/py2cytoscape
|
py2cytoscape/data/base_view.py
|
BaseView.set_value
|
def set_value(self, visual_property, value):
"""Set a single Visual Property Value
:param visual_property: Visual Property ID
:param value: New value for the VP
:return: None
"""
if visual_property is None or value is None:
raise ValueError('Both VP and value are required.')
new_value = [
{
'visualProperty': visual_property,
"value": value
}
]
requests.put(self.url, data=json.dumps(new_value), headers=HEADERS)
|
python
|
def set_value(self, visual_property, value):
"""Set a single Visual Property Value
:param visual_property: Visual Property ID
:param value: New value for the VP
:return: None
"""
if visual_property is None or value is None:
raise ValueError('Both VP and value are required.')
new_value = [
{
'visualProperty': visual_property,
"value": value
}
]
requests.put(self.url, data=json.dumps(new_value), headers=HEADERS)
|
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Set a single Visual Property Value
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:return: None
|
[
"Set",
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"Value"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/base_view.py#L41-L57
|
12,073
|
cytoscape/py2cytoscape
|
py2cytoscape/data/base_view.py
|
BaseView.set_values
|
def set_values(self, values):
"""
Set multiple Visual properties at once.
:param values:
:return:
"""
if values is None:
raise ValueError('Values are required.')
new_values = []
for vp in values.keys():
new_val = {
'visualProperty': vp,
'value': values[vp]
}
new_values.append(new_val)
requests.put(self.url, data=json.dumps(new_values), headers=HEADERS)
|
python
|
def set_values(self, values):
"""
Set multiple Visual properties at once.
:param values:
:return:
"""
if values is None:
raise ValueError('Values are required.')
new_values = []
for vp in values.keys():
new_val = {
'visualProperty': vp,
'value': values[vp]
}
new_values.append(new_val)
requests.put(self.url, data=json.dumps(new_values), headers=HEADERS)
|
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Set multiple Visual properties at once.
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|
[
"Set",
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"Visual",
"properties",
"at",
"once",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/base_view.py#L59-L77
|
12,074
|
cytoscape/py2cytoscape
|
py2cytoscape/data/base_view.py
|
BaseView.get_value
|
def get_value(self, visual_property):
"""Get a value for the Visual Property
:param visual_property:
:return:
"""
res = requests.get(self.url + '/' + visual_property)
return res.json()['value']
|
python
|
def get_value(self, visual_property):
"""Get a value for the Visual Property
:param visual_property:
:return:
"""
res = requests.get(self.url + '/' + visual_property)
return res.json()['value']
|
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Get a value for the Visual Property
:param visual_property:
:return:
|
[
"Get",
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] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/base_view.py#L79-L86
|
12,075
|
cytoscape/py2cytoscape
|
py2cytoscape/data/base_view.py
|
BaseView.get_values
|
def get_values(self):
"""Get all visual property values for the object
:return: dictionary of values (VP ID - value)
"""
results = requests.get(self.url).json()
values = {}
for entry in results:
values[entry['visualProperty']] = entry['value']
return values
|
python
|
def get_values(self):
"""Get all visual property values for the object
:return: dictionary of values (VP ID - value)
"""
results = requests.get(self.url).json()
values = {}
for entry in results:
values[entry['visualProperty']] = entry['value']
return values
|
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Get all visual property values for the object
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|
[
"Get",
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dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/base_view.py#L88-L98
|
12,076
|
cytoscape/py2cytoscape
|
py2cytoscape/data/network_view.py
|
CyNetworkView.update_network_view
|
def update_network_view(self, visual_property=None, value=None):
"""
Updates single value for Network-related VP.
:param visual_property:
:param value:
:return:
"""
new_value = [
{
"visualProperty": visual_property,
"value": value
}
]
res = requests.put(self.__url + '/network',
data=json.dumps(new_value),
headers=HEADERS)
check_response(res)
|
python
|
def update_network_view(self, visual_property=None, value=None):
"""
Updates single value for Network-related VP.
:param visual_property:
:param value:
:return:
"""
new_value = [
{
"visualProperty": visual_property,
"value": value
}
]
res = requests.put(self.__url + '/network',
data=json.dumps(new_value),
headers=HEADERS)
check_response(res)
|
[
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Updates single value for Network-related VP.
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|
[
"Updates",
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"-",
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"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/network_view.py#L153-L171
|
12,077
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/view.py
|
view.export
|
def export(self, Height=None, options=None, outputFile=None, Resolution=None,\
Units=None, Width=None, Zoom=None, view="current", verbose=False):
"""
Exports the current view to a graphics file and returns the path to the
saved file. PNG and JPEG formats have options for scaling, while other
formats only have the option 'exportTextAsFont'. For the PDF format,
exporting text as font does not work for two-byte characters such as
Chinese or Japanese. To avoid corrupted texts in the exported PDF,
please set false to 'exportTextAsFont' when exporting networks including
those non-English characters.
:param Height (string, optional): The height of the exported image. Valid
only for bitmap formats, such as PNG and JPEG.
:param options (string, optional): The format of the output file. =
['JPEG (*.jpeg, *.jpg)', 'PDF (*.pdf)', 'PNG (*.png)', 'PostScript (*.ps)',
'SVG (*.svg)']
:param OutputFile (string, optional): The path name of the file where
the view must be saved to. By default, the view's title is used as
the file name.
:param Resolution (string, optional): The resolution of the exported
image, in DPI. Valid only for bitmap formats, when the selected width
and height 'units' is inches. The possible values are: 72 (default),
100, 150, 300, 600. = ['72', '100', '150', '300', '600']
:param Units (string, optional): The units for the 'width' and 'height'
values. Valid only for bitmap formats, such as PNG and JPEG. The
possible values are: pixels (default), inches. = ['pixels', 'inches']
:param Width (string, optional): The width of the exported image. Valid
only for bitmap formats, such as PNG and JPEG.
:param Zoom (string, optional): The zoom value to proportionally scale
the image. The default value is 100.0. Valid only for bitmap formats,
such as PNG and JPEG
:param verbose: print more
:returns: path to the saved file
"""
PARAMS=set_param(["Height","options","outputFile","Resolution",\
"Units","Width","Zoom","view"],\
[Height,options,outputFile,Resolution,Units,Width,Zoom,view ])
response=api(url=self.__url+"/export", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def export(self, Height=None, options=None, outputFile=None, Resolution=None,\
Units=None, Width=None, Zoom=None, view="current", verbose=False):
"""
Exports the current view to a graphics file and returns the path to the
saved file. PNG and JPEG formats have options for scaling, while other
formats only have the option 'exportTextAsFont'. For the PDF format,
exporting text as font does not work for two-byte characters such as
Chinese or Japanese. To avoid corrupted texts in the exported PDF,
please set false to 'exportTextAsFont' when exporting networks including
those non-English characters.
:param Height (string, optional): The height of the exported image. Valid
only for bitmap formats, such as PNG and JPEG.
:param options (string, optional): The format of the output file. =
['JPEG (*.jpeg, *.jpg)', 'PDF (*.pdf)', 'PNG (*.png)', 'PostScript (*.ps)',
'SVG (*.svg)']
:param OutputFile (string, optional): The path name of the file where
the view must be saved to. By default, the view's title is used as
the file name.
:param Resolution (string, optional): The resolution of the exported
image, in DPI. Valid only for bitmap formats, when the selected width
and height 'units' is inches. The possible values are: 72 (default),
100, 150, 300, 600. = ['72', '100', '150', '300', '600']
:param Units (string, optional): The units for the 'width' and 'height'
values. Valid only for bitmap formats, such as PNG and JPEG. The
possible values are: pixels (default), inches. = ['pixels', 'inches']
:param Width (string, optional): The width of the exported image. Valid
only for bitmap formats, such as PNG and JPEG.
:param Zoom (string, optional): The zoom value to proportionally scale
the image. The default value is 100.0. Valid only for bitmap formats,
such as PNG and JPEG
:param verbose: print more
:returns: path to the saved file
"""
PARAMS=set_param(["Height","options","outputFile","Resolution",\
"Units","Width","Zoom","view"],\
[Height,options,outputFile,Resolution,Units,Width,Zoom,view ])
response=api(url=self.__url+"/export", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
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"PARAMS",
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"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Exports the current view to a graphics file and returns the path to the
saved file. PNG and JPEG formats have options for scaling, while other
formats only have the option 'exportTextAsFont'. For the PDF format,
exporting text as font does not work for two-byte characters such as
Chinese or Japanese. To avoid corrupted texts in the exported PDF,
please set false to 'exportTextAsFont' when exporting networks including
those non-English characters.
:param Height (string, optional): The height of the exported image. Valid
only for bitmap formats, such as PNG and JPEG.
:param options (string, optional): The format of the output file. =
['JPEG (*.jpeg, *.jpg)', 'PDF (*.pdf)', 'PNG (*.png)', 'PostScript (*.ps)',
'SVG (*.svg)']
:param OutputFile (string, optional): The path name of the file where
the view must be saved to. By default, the view's title is used as
the file name.
:param Resolution (string, optional): The resolution of the exported
image, in DPI. Valid only for bitmap formats, when the selected width
and height 'units' is inches. The possible values are: 72 (default),
100, 150, 300, 600. = ['72', '100', '150', '300', '600']
:param Units (string, optional): The units for the 'width' and 'height'
values. Valid only for bitmap formats, such as PNG and JPEG. The
possible values are: pixels (default), inches. = ['pixels', 'inches']
:param Width (string, optional): The width of the exported image. Valid
only for bitmap formats, such as PNG and JPEG.
:param Zoom (string, optional): The zoom value to proportionally scale
the image. The default value is 100.0. Valid only for bitmap formats,
such as PNG and JPEG
:param verbose: print more
:returns: path to the saved file
|
[
"Exports",
"the",
"current",
"view",
"to",
"a",
"graphics",
"file",
"and",
"returns",
"the",
"path",
"to",
"the",
"saved",
"file",
".",
"PNG",
"and",
"JPEG",
"formats",
"have",
"options",
"for",
"scaling",
"while",
"other",
"formats",
"only",
"have",
"the",
"option",
"exportTextAsFont",
".",
"For",
"the",
"PDF",
"format",
"exporting",
"text",
"as",
"font",
"does",
"not",
"work",
"for",
"two",
"-",
"byte",
"characters",
"such",
"as",
"Chinese",
"or",
"Japanese",
".",
"To",
"avoid",
"corrupted",
"texts",
"in",
"the",
"exported",
"PDF",
"please",
"set",
"false",
"to",
"exportTextAsFont",
"when",
"exporting",
"networks",
"including",
"those",
"non",
"-",
"English",
"characters",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/view.py#L46-L85
|
12,078
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/view.py
|
view.fit_content
|
def fit_content(self, verbose=False):
"""
Zooms out the current view in order to display all of its elements.
:param verbose: print more
"""
PARAMS={}
response=api(url=self.__url+"/fit content", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def fit_content(self, verbose=False):
"""
Zooms out the current view in order to display all of its elements.
:param verbose: print more
"""
PARAMS={}
response=api(url=self.__url+"/fit content", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
"def",
"fit_content",
"(",
"self",
",",
"verbose",
"=",
"False",
")",
":",
"PARAMS",
"=",
"{",
"}",
"response",
"=",
"api",
"(",
"url",
"=",
"self",
".",
"__url",
"+",
"\"/fit content\"",
",",
"PARAMS",
"=",
"PARAMS",
",",
"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Zooms out the current view in order to display all of its elements.
:param verbose: print more
|
[
"Zooms",
"out",
"the",
"current",
"view",
"in",
"order",
"to",
"display",
"all",
"of",
"its",
"elements",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/view.py#L87-L96
|
12,079
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/view.py
|
view.get_current
|
def get_current(self, layout=None, network=None, verbose=False):
"""
Returns the current view or null if there is none.
:param verbose: print more
:returns: current view or null if there is none
"""
PARAMS={}
response=api(url=self.__url+"/get_current", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def get_current(self, layout=None, network=None, verbose=False):
"""
Returns the current view or null if there is none.
:param verbose: print more
:returns: current view or null if there is none
"""
PARAMS={}
response=api(url=self.__url+"/get_current", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
"def",
"get_current",
"(",
"self",
",",
"layout",
"=",
"None",
",",
"network",
"=",
"None",
",",
"verbose",
"=",
"False",
")",
":",
"PARAMS",
"=",
"{",
"}",
"response",
"=",
"api",
"(",
"url",
"=",
"self",
".",
"__url",
"+",
"\"/get_current\"",
",",
"PARAMS",
"=",
"PARAMS",
",",
"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Returns the current view or null if there is none.
:param verbose: print more
:returns: current view or null if there is none
|
[
"Returns",
"the",
"current",
"view",
"or",
"null",
"if",
"there",
"is",
"none",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/view.py#L110-L120
|
12,080
|
cytoscape/py2cytoscape
|
py2cytoscape/data/style.py
|
Style.update_defaults
|
def update_defaults(self, prop_value_dict):
"""
Updates the value of one or more visual properties.
:param prop_value_dict: Dictionary containing, for each visual property,
the new value to use.
"""
body = []
for key in prop_value_dict:
entry = {
'visualProperty': key,
'value': prop_value_dict[key]
}
body.append(entry)
url = self.__url + 'defaults'
requests.put(url, data=json.dumps(body), headers=HEADERS)
|
python
|
def update_defaults(self, prop_value_dict):
"""
Updates the value of one or more visual properties.
:param prop_value_dict: Dictionary containing, for each visual property,
the new value to use.
"""
body = []
for key in prop_value_dict:
entry = {
'visualProperty': key,
'value': prop_value_dict[key]
}
body.append(entry)
url = self.__url + 'defaults'
requests.put(url, data=json.dumps(body), headers=HEADERS)
|
[
"def",
"update_defaults",
"(",
"self",
",",
"prop_value_dict",
")",
":",
"body",
"=",
"[",
"]",
"for",
"key",
"in",
"prop_value_dict",
":",
"entry",
"=",
"{",
"'visualProperty'",
":",
"key",
",",
"'value'",
":",
"prop_value_dict",
"[",
"key",
"]",
"}",
"body",
".",
"append",
"(",
"entry",
")",
"url",
"=",
"self",
".",
"__url",
"+",
"'defaults'",
"requests",
".",
"put",
"(",
"url",
",",
"data",
"=",
"json",
".",
"dumps",
"(",
"body",
")",
",",
"headers",
"=",
"HEADERS",
")"
] |
Updates the value of one or more visual properties.
:param prop_value_dict: Dictionary containing, for each visual property,
the new value to use.
|
[
"Updates",
"the",
"value",
"of",
"one",
"or",
"more",
"visual",
"properties",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/data/style.py#L112-L129
|
12,081
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/cyrest.py
|
cyclient.status
|
def status(self, verbose=False):
"""
Checks the status of your CyREST server.
"""
try:
response=api(url=self.__url, method="GET", verbose=verbose)
except Exception as e:
print('Could not get status from CyREST:\n\n' + str(e))
else:
print('CyREST online!')
|
python
|
def status(self, verbose=False):
"""
Checks the status of your CyREST server.
"""
try:
response=api(url=self.__url, method="GET", verbose=verbose)
except Exception as e:
print('Could not get status from CyREST:\n\n' + str(e))
else:
print('CyREST online!')
|
[
"def",
"status",
"(",
"self",
",",
"verbose",
"=",
"False",
")",
":",
"try",
":",
"response",
"=",
"api",
"(",
"url",
"=",
"self",
".",
"__url",
",",
"method",
"=",
"\"GET\"",
",",
"verbose",
"=",
"verbose",
")",
"except",
"Exception",
"as",
"e",
":",
"print",
"(",
"'Could not get status from CyREST:\\n\\n'",
"+",
"str",
"(",
"e",
")",
")",
"else",
":",
"print",
"(",
"'CyREST online!'",
")"
] |
Checks the status of your CyREST server.
|
[
"Checks",
"the",
"status",
"of",
"your",
"CyREST",
"server",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/cyrest.py#L67-L76
|
12,082
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/cyrest.py
|
cyclient.version
|
def version(self, verbose=False):
"""
Checks Cytoscape version
"""
response=api(url=self.__url+"version",method="H", verbose=verbose)
response=json.loads(response)
for k in response.keys():
print(k, response[k])
|
python
|
def version(self, verbose=False):
"""
Checks Cytoscape version
"""
response=api(url=self.__url+"version",method="H", verbose=verbose)
response=json.loads(response)
for k in response.keys():
print(k, response[k])
|
[
"def",
"version",
"(",
"self",
",",
"verbose",
"=",
"False",
")",
":",
"response",
"=",
"api",
"(",
"url",
"=",
"self",
".",
"__url",
"+",
"\"version\"",
",",
"method",
"=",
"\"H\"",
",",
"verbose",
"=",
"verbose",
")",
"response",
"=",
"json",
".",
"loads",
"(",
"response",
")",
"for",
"k",
"in",
"response",
".",
"keys",
"(",
")",
":",
"print",
"(",
"k",
",",
"response",
"[",
"k",
"]",
")"
] |
Checks Cytoscape version
|
[
"Checks",
"Cytoscape",
"version"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/cyrest.py#L84-L91
|
12,083
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/idmapper.py
|
idmapper.map_column
|
def map_column(self, only_use_one=None, source_column=None, species=None, target_selection= None, verbose=False):
"""
Uses the BridgeDB service to look up analogous identifiers from a wide
selection of other databases
:param only_use_one (string, optional): When multiple identifiers can be
mapped from a single term, this forces a singular result
:param source_column (string): Specifies the column nmae where the
source identifiers are located = ['']
:param source_selection (string): Specifies the database describing
the existing identifiers = ['']
:param species (string, optional): The combined common or latin name of
the species to which the identifiers apply = ['Human (Homo sapiens)',
'Mouse (Mus musculus)', 'Rat (Rattus norvegicus)', 'Frog (Xenopus tropicalis)',
'Zebra fish (Danio rerio)', 'Fruit fly (Drosophila melanogaster)',
'Mosquito (Anopheles gambiae)', 'Arabidopsis thaliana (Arabidopsis thaliana)',
'Yeast (Saccharomyces cerevisiae)', 'E. coli (Escherichia coli)',
'Tuberculosis (Mycobacterium tuberculosis)', 'Worm (Caenorhabditis elegans)']
:param target_selection (string): Specifies the database identifiers to be looked up = ['']
:param verbose: print more
:returns: eg. { "new column": "SGD " }
"""
PARAMS=set_param(["only_use_one","source_column","species","target_selection"],[only_use_one,source_column,species,target_selection])
response=api(url=self.__url+"/map column", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
python
|
def map_column(self, only_use_one=None, source_column=None, species=None, target_selection= None, verbose=False):
"""
Uses the BridgeDB service to look up analogous identifiers from a wide
selection of other databases
:param only_use_one (string, optional): When multiple identifiers can be
mapped from a single term, this forces a singular result
:param source_column (string): Specifies the column nmae where the
source identifiers are located = ['']
:param source_selection (string): Specifies the database describing
the existing identifiers = ['']
:param species (string, optional): The combined common or latin name of
the species to which the identifiers apply = ['Human (Homo sapiens)',
'Mouse (Mus musculus)', 'Rat (Rattus norvegicus)', 'Frog (Xenopus tropicalis)',
'Zebra fish (Danio rerio)', 'Fruit fly (Drosophila melanogaster)',
'Mosquito (Anopheles gambiae)', 'Arabidopsis thaliana (Arabidopsis thaliana)',
'Yeast (Saccharomyces cerevisiae)', 'E. coli (Escherichia coli)',
'Tuberculosis (Mycobacterium tuberculosis)', 'Worm (Caenorhabditis elegans)']
:param target_selection (string): Specifies the database identifiers to be looked up = ['']
:param verbose: print more
:returns: eg. { "new column": "SGD " }
"""
PARAMS=set_param(["only_use_one","source_column","species","target_selection"],[only_use_one,source_column,species,target_selection])
response=api(url=self.__url+"/map column", PARAMS=PARAMS, method="POST", verbose=verbose)
return response
|
[
"def",
"map_column",
"(",
"self",
",",
"only_use_one",
"=",
"None",
",",
"source_column",
"=",
"None",
",",
"species",
"=",
"None",
",",
"target_selection",
"=",
"None",
",",
"verbose",
"=",
"False",
")",
":",
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"=",
"set_param",
"(",
"[",
"\"only_use_one\"",
",",
"\"source_column\"",
",",
"\"species\"",
",",
"\"target_selection\"",
"]",
",",
"[",
"only_use_one",
",",
"source_column",
",",
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"target_selection",
"]",
")",
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"api",
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"+",
"\"/map column\"",
",",
"PARAMS",
"=",
"PARAMS",
",",
"method",
"=",
"\"POST\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
Uses the BridgeDB service to look up analogous identifiers from a wide
selection of other databases
:param only_use_one (string, optional): When multiple identifiers can be
mapped from a single term, this forces a singular result
:param source_column (string): Specifies the column nmae where the
source identifiers are located = ['']
:param source_selection (string): Specifies the database describing
the existing identifiers = ['']
:param species (string, optional): The combined common or latin name of
the species to which the identifiers apply = ['Human (Homo sapiens)',
'Mouse (Mus musculus)', 'Rat (Rattus norvegicus)', 'Frog (Xenopus tropicalis)',
'Zebra fish (Danio rerio)', 'Fruit fly (Drosophila melanogaster)',
'Mosquito (Anopheles gambiae)', 'Arabidopsis thaliana (Arabidopsis thaliana)',
'Yeast (Saccharomyces cerevisiae)', 'E. coli (Escherichia coli)',
'Tuberculosis (Mycobacterium tuberculosis)', 'Worm (Caenorhabditis elegans)']
:param target_selection (string): Specifies the database identifiers to be looked up = ['']
:param verbose: print more
:returns: eg. { "new column": "SGD " }
|
[
"Uses",
"the",
"BridgeDB",
"service",
"to",
"look",
"up",
"analogous",
"identifiers",
"from",
"a",
"wide",
"selection",
"of",
"other",
"databases"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/idmapper.py#L13-L38
|
12,084
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/command.py
|
command.echo
|
def echo(self, variableName, verbose=False):
"""
The echo command will display the value of the variable specified by the
variableName argument, or all variables if variableName is not provided.
:param variableName: The name of the variable or '*' to display the value of all variables.
:param verbose: print more
"""
PARAMS={"variableName":variableName}
response=api(url=self.__url+"/echo", PARAMS=PARAMS, verbose=verbose)
return response
|
python
|
def echo(self, variableName, verbose=False):
"""
The echo command will display the value of the variable specified by the
variableName argument, or all variables if variableName is not provided.
:param variableName: The name of the variable or '*' to display the value of all variables.
:param verbose: print more
"""
PARAMS={"variableName":variableName}
response=api(url=self.__url+"/echo", PARAMS=PARAMS, verbose=verbose)
return response
|
[
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"PARAMS",
"=",
"PARAMS",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
The echo command will display the value of the variable specified by the
variableName argument, or all variables if variableName is not provided.
:param variableName: The name of the variable or '*' to display the value of all variables.
:param verbose: print more
|
[
"The",
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"or",
"all",
"variables",
"if",
"variableName",
"is",
"not",
"provided",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/command.py#L13-L23
|
12,085
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/command.py
|
command.open_dialog
|
def open_dialog(self, verbose=False):
"""
The command line dialog provides a field to enter commands and view
results. It also provides the help command to display namespaces,
commands, and arguments.
:param verbose: print more
"""
response=api(url=self.__url+"/open dialog", verbose=verbose)
return response
|
python
|
def open_dialog(self, verbose=False):
"""
The command line dialog provides a field to enter commands and view
results. It also provides the help command to display namespaces,
commands, and arguments.
:param verbose: print more
"""
response=api(url=self.__url+"/open dialog", verbose=verbose)
return response
|
[
"def",
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"False",
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"__url",
"+",
"\"/open dialog\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
The command line dialog provides a field to enter commands and view
results. It also provides the help command to display namespaces,
commands, and arguments.
:param verbose: print more
|
[
"The",
"command",
"line",
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"to",
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"the",
"help",
"command",
"to",
"display",
"namespaces",
"commands",
"and",
"arguments",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/command.py#L25-L34
|
12,086
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/command.py
|
command.pause
|
def pause(self, message=None, verbose=False):
"""
The pause command displays a dialog with the text provided in the
message argument and waits for the user to click OK
:param message: a message to display. default=None
:param verbose: print more
"""
PARAMS=set_param(["message"],[message])
response=api(url=self.__url+"/pause", PARAMS=PARAMS, verbose=verbose)
return response
|
python
|
def pause(self, message=None, verbose=False):
"""
The pause command displays a dialog with the text provided in the
message argument and waits for the user to click OK
:param message: a message to display. default=None
:param verbose: print more
"""
PARAMS=set_param(["message"],[message])
response=api(url=self.__url+"/pause", PARAMS=PARAMS, verbose=verbose)
return response
|
[
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"self",
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"None",
",",
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"=",
"False",
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"\"/pause\"",
",",
"PARAMS",
"=",
"PARAMS",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
The pause command displays a dialog with the text provided in the
message argument and waits for the user to click OK
:param message: a message to display. default=None
:param verbose: print more
|
[
"The",
"pause",
"command",
"displays",
"a",
"dialog",
"with",
"the",
"text",
"provided",
"in",
"the",
"message",
"argument",
"and",
"waits",
"for",
"the",
"user",
"to",
"click",
"OK"
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/command.py#L37-L48
|
12,087
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/command.py
|
command.quit
|
def quit(self,verbose=False):
"""
This command causes Cytoscape to exit. It is typically used at the end
of a script file.
:param verbose: print more
"""
response=api(url=self.__url+"/quit", verbose=verbose)
return response
|
python
|
def quit(self,verbose=False):
"""
This command causes Cytoscape to exit. It is typically used at the end
of a script file.
:param verbose: print more
"""
response=api(url=self.__url+"/quit", verbose=verbose)
return response
|
[
"def",
"quit",
"(",
"self",
",",
"verbose",
"=",
"False",
")",
":",
"response",
"=",
"api",
"(",
"url",
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"self",
".",
"__url",
"+",
"\"/quit\"",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
This command causes Cytoscape to exit. It is typically used at the end
of a script file.
:param verbose: print more
|
[
"This",
"command",
"causes",
"Cytoscape",
"to",
"exit",
".",
"It",
"is",
"typically",
"used",
"at",
"the",
"end",
"of",
"a",
"script",
"file",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/command.py#L51-L59
|
12,088
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/command.py
|
command.run
|
def run(self,script_file,args=None,verbose=False):
"""
The run command will execute a command script from the file pointed to
by the file argument, which should contain Cytoscape commands, one per
line. Arguments to the script are provided by the args argument.
:param script_file: file to run
:param args: enter the script arguments as key:value pairs separated by
commas. eg. "arg1:value1,arg2:value2"
:param verbose: print more
"""
PARAMS=set_param(["file","args"],[script_file,args])
response=api(url=self.__url+"/run", PARAMS=PARAMS, verbose=verbose)
return response
|
python
|
def run(self,script_file,args=None,verbose=False):
"""
The run command will execute a command script from the file pointed to
by the file argument, which should contain Cytoscape commands, one per
line. Arguments to the script are provided by the args argument.
:param script_file: file to run
:param args: enter the script arguments as key:value pairs separated by
commas. eg. "arg1:value1,arg2:value2"
:param verbose: print more
"""
PARAMS=set_param(["file","args"],[script_file,args])
response=api(url=self.__url+"/run", PARAMS=PARAMS, verbose=verbose)
return response
|
[
"def",
"run",
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"self",
",",
"script_file",
",",
"args",
"=",
"None",
",",
"verbose",
"=",
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"=",
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",",
"PARAMS",
"=",
"PARAMS",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
The run command will execute a command script from the file pointed to
by the file argument, which should contain Cytoscape commands, one per
line. Arguments to the script are provided by the args argument.
:param script_file: file to run
:param args: enter the script arguments as key:value pairs separated by
commas. eg. "arg1:value1,arg2:value2"
:param verbose: print more
|
[
"The",
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"a",
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"script",
"from",
"the",
"file",
"pointed",
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"which",
"should",
"contain",
"Cytoscape",
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"one",
"per",
"line",
".",
"Arguments",
"to",
"the",
"script",
"are",
"provided",
"by",
"the",
"args",
"argument",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/command.py#L61-L75
|
12,089
|
cytoscape/py2cytoscape
|
py2cytoscape/cyrest/command.py
|
command.sleep
|
def sleep(self,duration,verbose=False):
"""
The sleep command will pause processing for a period of time as specified
by duration seconds. It is typically used as part of a command script.
:param duration: enter the time in seconds to sleep
:param verbose: print more
"""
PARAMS={"duration":str(duration)}
response=api(url=self.__url+"/sleep", PARAMS=PARAMS, verbose=verbose)
return response
|
python
|
def sleep(self,duration,verbose=False):
"""
The sleep command will pause processing for a period of time as specified
by duration seconds. It is typically used as part of a command script.
:param duration: enter the time in seconds to sleep
:param verbose: print more
"""
PARAMS={"duration":str(duration)}
response=api(url=self.__url+"/sleep", PARAMS=PARAMS, verbose=verbose)
return response
|
[
"def",
"sleep",
"(",
"self",
",",
"duration",
",",
"verbose",
"=",
"False",
")",
":",
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"\"duration\"",
":",
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"duration",
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"__url",
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"\"/sleep\"",
",",
"PARAMS",
"=",
"PARAMS",
",",
"verbose",
"=",
"verbose",
")",
"return",
"response"
] |
The sleep command will pause processing for a period of time as specified
by duration seconds. It is typically used as part of a command script.
:param duration: enter the time in seconds to sleep
:param verbose: print more
|
[
"The",
"sleep",
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"will",
"pause",
"processing",
"for",
"a",
"period",
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"It",
"is",
"typically",
"used",
"as",
"part",
"of",
"a",
"command",
"script",
"."
] |
dd34de8d028f512314d0057168df7fef7c5d5195
|
https://github.com/cytoscape/py2cytoscape/blob/dd34de8d028f512314d0057168df7fef7c5d5195/py2cytoscape/cyrest/command.py#L77-L87
|
12,090
|
ofw/curlify
|
curlify.py
|
to_curl
|
def to_curl(request, compressed=False, verify=True):
"""
Returns string with curl command by provided request object
Parameters
----------
compressed : bool
If `True` then `--compressed` argument will be added to result
"""
parts = [
('curl', None),
('-X', request.method),
]
for k, v in sorted(request.headers.items()):
parts += [('-H', '{0}: {1}'.format(k, v))]
if request.body:
body = request.body
if isinstance(body, bytes):
body = body.decode('utf-8')
parts += [('-d', body)]
if compressed:
parts += [('--compressed', None)]
if not verify:
parts += [('--insecure', None)]
parts += [(None, request.url)]
flat_parts = []
for k, v in parts:
if k:
flat_parts.append(k)
if v:
flat_parts.append("'{0}'".format(v))
return ' '.join(flat_parts)
|
python
|
def to_curl(request, compressed=False, verify=True):
"""
Returns string with curl command by provided request object
Parameters
----------
compressed : bool
If `True` then `--compressed` argument will be added to result
"""
parts = [
('curl', None),
('-X', request.method),
]
for k, v in sorted(request.headers.items()):
parts += [('-H', '{0}: {1}'.format(k, v))]
if request.body:
body = request.body
if isinstance(body, bytes):
body = body.decode('utf-8')
parts += [('-d', body)]
if compressed:
parts += [('--compressed', None)]
if not verify:
parts += [('--insecure', None)]
parts += [(None, request.url)]
flat_parts = []
for k, v in parts:
if k:
flat_parts.append(k)
if v:
flat_parts.append("'{0}'".format(v))
return ' '.join(flat_parts)
|
[
"def",
"to_curl",
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"request",
",",
"compressed",
"=",
"False",
",",
"verify",
"=",
"True",
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"=",
"[",
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"(",
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".",
"format",
"(",
"v",
")",
")",
"return",
"' '",
".",
"join",
"(",
"flat_parts",
")"
] |
Returns string with curl command by provided request object
Parameters
----------
compressed : bool
If `True` then `--compressed` argument will be added to result
|
[
"Returns",
"string",
"with",
"curl",
"command",
"by",
"provided",
"request",
"object"
] |
5a464218431f979ac78d089682d36860b57420ce
|
https://github.com/ofw/curlify/blob/5a464218431f979ac78d089682d36860b57420ce/curlify.py#L4-L42
|
12,091
|
rq/Flask-RQ2
|
src/flask_rq2/cli.py
|
shared_options
|
def shared_options(rq):
"Default class options to pass to the CLI commands."
return {
'url': rq.redis_url,
'config': None,
'worker_class': rq.worker_class,
'job_class': rq.job_class,
'queue_class': rq.queue_class,
'connection_class': rq.connection_class,
}
|
python
|
def shared_options(rq):
"Default class options to pass to the CLI commands."
return {
'url': rq.redis_url,
'config': None,
'worker_class': rq.worker_class,
'job_class': rq.job_class,
'queue_class': rq.queue_class,
'connection_class': rq.connection_class,
}
|
[
"def",
"shared_options",
"(",
"rq",
")",
":",
"return",
"{",
"'url'",
":",
"rq",
".",
"redis_url",
",",
"'config'",
":",
"None",
",",
"'worker_class'",
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".",
"worker_class",
",",
"'job_class'",
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"job_class",
",",
"'queue_class'",
":",
"rq",
".",
"queue_class",
",",
"'connection_class'",
":",
"rq",
".",
"connection_class",
",",
"}"
] |
Default class options to pass to the CLI commands.
|
[
"Default",
"class",
"options",
"to",
"pass",
"to",
"the",
"CLI",
"commands",
"."
] |
58eedf6f0cd7bcde4ccd787074762ea08f531337
|
https://github.com/rq/Flask-RQ2/blob/58eedf6f0cd7bcde4ccd787074762ea08f531337/src/flask_rq2/cli.py#L35-L44
|
12,092
|
rq/Flask-RQ2
|
src/flask_rq2/cli.py
|
empty
|
def empty(rq, ctx, all, queues):
"Empty given queues."
return ctx.invoke(
rq_cli.empty,
all=all,
queues=queues or rq.queues,
**shared_options(rq)
)
|
python
|
def empty(rq, ctx, all, queues):
"Empty given queues."
return ctx.invoke(
rq_cli.empty,
all=all,
queues=queues or rq.queues,
**shared_options(rq)
)
|
[
"def",
"empty",
"(",
"rq",
",",
"ctx",
",",
"all",
",",
"queues",
")",
":",
"return",
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"invoke",
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"rq_cli",
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"empty",
",",
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"=",
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"or",
"rq",
".",
"queues",
",",
"*",
"*",
"shared_options",
"(",
"rq",
")",
")"
] |
Empty given queues.
|
[
"Empty",
"given",
"queues",
"."
] |
58eedf6f0cd7bcde4ccd787074762ea08f531337
|
https://github.com/rq/Flask-RQ2/blob/58eedf6f0cd7bcde4ccd787074762ea08f531337/src/flask_rq2/cli.py#L66-L73
|
12,093
|
rq/Flask-RQ2
|
src/flask_rq2/cli.py
|
requeue
|
def requeue(rq, ctx, all, job_ids):
"Requeue failed jobs."
return ctx.invoke(
rq_cli.requeue,
all=all,
job_ids=job_ids,
**shared_options(rq)
)
|
python
|
def requeue(rq, ctx, all, job_ids):
"Requeue failed jobs."
return ctx.invoke(
rq_cli.requeue,
all=all,
job_ids=job_ids,
**shared_options(rq)
)
|
[
"def",
"requeue",
"(",
"rq",
",",
"ctx",
",",
"all",
",",
"job_ids",
")",
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"requeue",
",",
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",",
"job_ids",
"=",
"job_ids",
",",
"*",
"*",
"shared_options",
"(",
"rq",
")",
")"
] |
Requeue failed jobs.
|
[
"Requeue",
"failed",
"jobs",
"."
] |
58eedf6f0cd7bcde4ccd787074762ea08f531337
|
https://github.com/rq/Flask-RQ2/blob/58eedf6f0cd7bcde4ccd787074762ea08f531337/src/flask_rq2/cli.py#L79-L86
|
12,094
|
rq/Flask-RQ2
|
src/flask_rq2/cli.py
|
info
|
def info(rq, ctx, path, interval, raw, only_queues, only_workers, by_queue,
queues):
"RQ command-line monitor."
return ctx.invoke(
rq_cli.info,
path=path,
interval=interval,
raw=raw,
only_queues=only_queues,
only_workers=only_workers,
by_queue=by_queue,
queues=queues or rq.queues,
**shared_options(rq)
)
|
python
|
def info(rq, ctx, path, interval, raw, only_queues, only_workers, by_queue,
queues):
"RQ command-line monitor."
return ctx.invoke(
rq_cli.info,
path=path,
interval=interval,
raw=raw,
only_queues=only_queues,
only_workers=only_workers,
by_queue=by_queue,
queues=queues or rq.queues,
**shared_options(rq)
)
|
[
"def",
"info",
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",",
"ctx",
",",
"path",
",",
"interval",
",",
"raw",
",",
"only_queues",
",",
"only_workers",
",",
"by_queue",
",",
"queues",
")",
":",
"return",
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".",
"invoke",
"(",
"rq_cli",
".",
"info",
",",
"path",
"=",
"path",
",",
"interval",
"=",
"interval",
",",
"raw",
"=",
"raw",
",",
"only_queues",
"=",
"only_queues",
",",
"only_workers",
"=",
"only_workers",
",",
"by_queue",
"=",
"by_queue",
",",
"queues",
"=",
"queues",
"or",
"rq",
".",
"queues",
",",
"*",
"*",
"shared_options",
"(",
"rq",
")",
")"
] |
RQ command-line monitor.
|
[
"RQ",
"command",
"-",
"line",
"monitor",
"."
] |
58eedf6f0cd7bcde4ccd787074762ea08f531337
|
https://github.com/rq/Flask-RQ2/blob/58eedf6f0cd7bcde4ccd787074762ea08f531337/src/flask_rq2/cli.py#L100-L113
|
12,095
|
rq/Flask-RQ2
|
src/flask_rq2/cli.py
|
worker
|
def worker(rq, ctx, burst, logging_level, name, path, results_ttl,
worker_ttl, verbose, quiet, sentry_dsn, exception_handler, pid,
queues):
"Starts an RQ worker."
ctx.invoke(
rq_cli.worker,
burst=burst,
logging_level=logging_level,
name=name,
path=path,
results_ttl=results_ttl,
worker_ttl=worker_ttl,
verbose=verbose,
quiet=quiet,
sentry_dsn=sentry_dsn,
exception_handler=exception_handler or rq._exception_handlers,
pid=pid,
queues=queues or rq.queues,
**shared_options(rq)
)
|
python
|
def worker(rq, ctx, burst, logging_level, name, path, results_ttl,
worker_ttl, verbose, quiet, sentry_dsn, exception_handler, pid,
queues):
"Starts an RQ worker."
ctx.invoke(
rq_cli.worker,
burst=burst,
logging_level=logging_level,
name=name,
path=path,
results_ttl=results_ttl,
worker_ttl=worker_ttl,
verbose=verbose,
quiet=quiet,
sentry_dsn=sentry_dsn,
exception_handler=exception_handler or rq._exception_handlers,
pid=pid,
queues=queues or rq.queues,
**shared_options(rq)
)
|
[
"def",
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"(",
"rq",
",",
"ctx",
",",
"burst",
",",
"logging_level",
",",
"name",
",",
"path",
",",
"results_ttl",
",",
"worker_ttl",
",",
"verbose",
",",
"quiet",
",",
"sentry_dsn",
",",
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",",
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",",
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",",
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"=",
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",",
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"=",
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"or",
"rq",
".",
"queues",
",",
"*",
"*",
"shared_options",
"(",
"rq",
")",
")"
] |
Starts an RQ worker.
|
[
"Starts",
"an",
"RQ",
"worker",
"."
] |
58eedf6f0cd7bcde4ccd787074762ea08f531337
|
https://github.com/rq/Flask-RQ2/blob/58eedf6f0cd7bcde4ccd787074762ea08f531337/src/flask_rq2/cli.py#L136-L155
|
12,096
|
rq/Flask-RQ2
|
src/flask_rq2/cli.py
|
suspend
|
def suspend(rq, ctx, duration):
"Suspends all workers."
ctx.invoke(
rq_cli.suspend,
duration=duration,
**shared_options(rq)
)
|
python
|
def suspend(rq, ctx, duration):
"Suspends all workers."
ctx.invoke(
rq_cli.suspend,
duration=duration,
**shared_options(rq)
)
|
[
"def",
"suspend",
"(",
"rq",
",",
"ctx",
",",
"duration",
")",
":",
"ctx",
".",
"invoke",
"(",
"rq_cli",
".",
"suspend",
",",
"duration",
"=",
"duration",
",",
"*",
"*",
"shared_options",
"(",
"rq",
")",
")"
] |
Suspends all workers.
|
[
"Suspends",
"all",
"workers",
"."
] |
58eedf6f0cd7bcde4ccd787074762ea08f531337
|
https://github.com/rq/Flask-RQ2/blob/58eedf6f0cd7bcde4ccd787074762ea08f531337/src/flask_rq2/cli.py#L162-L168
|
12,097
|
rq/Flask-RQ2
|
src/flask_rq2/cli.py
|
scheduler
|
def scheduler(rq, ctx, verbose, burst, queue, interval, pid):
"Periodically checks for scheduled jobs."
scheduler = rq.get_scheduler(interval=interval, queue=queue)
if pid:
with open(os.path.expanduser(pid), 'w') as fp:
fp.write(str(os.getpid()))
if verbose:
level = 'DEBUG'
else:
level = 'INFO'
setup_loghandlers(level)
scheduler.run(burst=burst)
|
python
|
def scheduler(rq, ctx, verbose, burst, queue, interval, pid):
"Periodically checks for scheduled jobs."
scheduler = rq.get_scheduler(interval=interval, queue=queue)
if pid:
with open(os.path.expanduser(pid), 'w') as fp:
fp.write(str(os.getpid()))
if verbose:
level = 'DEBUG'
else:
level = 'INFO'
setup_loghandlers(level)
scheduler.run(burst=burst)
|
[
"def",
"scheduler",
"(",
"rq",
",",
"ctx",
",",
"verbose",
",",
"burst",
",",
"queue",
",",
"interval",
",",
"pid",
")",
":",
"scheduler",
"=",
"rq",
".",
"get_scheduler",
"(",
"interval",
"=",
"interval",
",",
"queue",
"=",
"queue",
")",
"if",
"pid",
":",
"with",
"open",
"(",
"os",
".",
"path",
".",
"expanduser",
"(",
"pid",
")",
",",
"'w'",
")",
"as",
"fp",
":",
"fp",
".",
"write",
"(",
"str",
"(",
"os",
".",
"getpid",
"(",
")",
")",
")",
"if",
"verbose",
":",
"level",
"=",
"'DEBUG'",
"else",
":",
"level",
"=",
"'INFO'",
"setup_loghandlers",
"(",
"level",
")",
"scheduler",
".",
"run",
"(",
"burst",
"=",
"burst",
")"
] |
Periodically checks for scheduled jobs.
|
[
"Periodically",
"checks",
"for",
"scheduled",
"jobs",
"."
] |
58eedf6f0cd7bcde4ccd787074762ea08f531337
|
https://github.com/rq/Flask-RQ2/blob/58eedf6f0cd7bcde4ccd787074762ea08f531337/src/flask_rq2/cli.py#L193-L204
|
12,098
|
rq/Flask-RQ2
|
src/flask_rq2/app.py
|
RQ.init_cli
|
def init_cli(self, app):
"""
Initialize the Flask CLI support in case it was enabled for the
app.
Works with both Flask>=1.0's CLI support as well as the backport
in the Flask-CLI package for Flask<1.0.
"""
# in case click isn't installed after all
if click is None:
raise RuntimeError('Cannot import click. Is it installed?')
# only add commands if we have a click context available
from .cli import add_commands
add_commands(app.cli, self)
|
python
|
def init_cli(self, app):
"""
Initialize the Flask CLI support in case it was enabled for the
app.
Works with both Flask>=1.0's CLI support as well as the backport
in the Flask-CLI package for Flask<1.0.
"""
# in case click isn't installed after all
if click is None:
raise RuntimeError('Cannot import click. Is it installed?')
# only add commands if we have a click context available
from .cli import add_commands
add_commands(app.cli, self)
|
[
"def",
"init_cli",
"(",
"self",
",",
"app",
")",
":",
"# in case click isn't installed after all",
"if",
"click",
"is",
"None",
":",
"raise",
"RuntimeError",
"(",
"'Cannot import click. Is it installed?'",
")",
"# only add commands if we have a click context available",
"from",
".",
"cli",
"import",
"add_commands",
"add_commands",
"(",
"app",
".",
"cli",
",",
"self",
")"
] |
Initialize the Flask CLI support in case it was enabled for the
app.
Works with both Flask>=1.0's CLI support as well as the backport
in the Flask-CLI package for Flask<1.0.
|
[
"Initialize",
"the",
"Flask",
"CLI",
"support",
"in",
"case",
"it",
"was",
"enabled",
"for",
"the",
"app",
"."
] |
58eedf6f0cd7bcde4ccd787074762ea08f531337
|
https://github.com/rq/Flask-RQ2/blob/58eedf6f0cd7bcde4ccd787074762ea08f531337/src/flask_rq2/app.py#L195-L208
|
12,099
|
ionelmc/python-remote-pdb
|
src/remote_pdb.py
|
set_trace
|
def set_trace(host=None, port=None, patch_stdstreams=False):
"""
Opens a remote PDB on first available port.
"""
if host is None:
host = os.environ.get('REMOTE_PDB_HOST', '127.0.0.1')
if port is None:
port = int(os.environ.get('REMOTE_PDB_PORT', '0'))
rdb = RemotePdb(host=host, port=port, patch_stdstreams=patch_stdstreams)
rdb.set_trace(frame=sys._getframe().f_back)
|
python
|
def set_trace(host=None, port=None, patch_stdstreams=False):
"""
Opens a remote PDB on first available port.
"""
if host is None:
host = os.environ.get('REMOTE_PDB_HOST', '127.0.0.1')
if port is None:
port = int(os.environ.get('REMOTE_PDB_PORT', '0'))
rdb = RemotePdb(host=host, port=port, patch_stdstreams=patch_stdstreams)
rdb.set_trace(frame=sys._getframe().f_back)
|
[
"def",
"set_trace",
"(",
"host",
"=",
"None",
",",
"port",
"=",
"None",
",",
"patch_stdstreams",
"=",
"False",
")",
":",
"if",
"host",
"is",
"None",
":",
"host",
"=",
"os",
".",
"environ",
".",
"get",
"(",
"'REMOTE_PDB_HOST'",
",",
"'127.0.0.1'",
")",
"if",
"port",
"is",
"None",
":",
"port",
"=",
"int",
"(",
"os",
".",
"environ",
".",
"get",
"(",
"'REMOTE_PDB_PORT'",
",",
"'0'",
")",
")",
"rdb",
"=",
"RemotePdb",
"(",
"host",
"=",
"host",
",",
"port",
"=",
"port",
",",
"patch_stdstreams",
"=",
"patch_stdstreams",
")",
"rdb",
".",
"set_trace",
"(",
"frame",
"=",
"sys",
".",
"_getframe",
"(",
")",
".",
"f_back",
")"
] |
Opens a remote PDB on first available port.
|
[
"Opens",
"a",
"remote",
"PDB",
"on",
"first",
"available",
"port",
"."
] |
152b4af3b8da282bbba1fc6b62f85d5cdf70be6e
|
https://github.com/ionelmc/python-remote-pdb/blob/152b4af3b8da282bbba1fc6b62f85d5cdf70be6e/src/remote_pdb.py#L121-L130
|
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