docstring stringlengths 52 499 | function stringlengths 67 35.2k | __index_level_0__ int64 52.6k 1.16M |
|---|---|---|
Fetches a single instance which has value `keyval`
for the attribute `key`.
Args:
keyval: The value of the attribute.
key (str, optional): The attribute to search by. By default,
it is 'id'.
Returns:
A model instance if found. Else None.
... | def get(cls, keyval, key='id', user_id=None):
if keyval is None:
return None
if (key in cls.__table__.columns
and cls.__table__.columns[key].primary_key):
# if user_id and hasattr(cls, 'user_id'):
# return cls.query.filter_by(id=keyval, us... | 842,738 |
Initializes a new instance, adds it to the db and commits
the transaction.
Args:
**kwargs: The keyword arguments for the init constructor.
Examples:
>>> user = User.create(name="Vicky", email="vicky@h.com")
>>> user.id
35 | def create(cls, **kwargs):
try:
return cls.add(cls.new(**kwargs))
except:
cls.session.rollback()
raise | 842,740 |
Batch method for creating a list of instances
Args:
list_of_kwargs(list of dicts): hereA list of dicts where
each dict denotes the keyword args that you would pass
to the create method separately
Examples:
>>> Customer.create_all([
.... | def create_all(cls, list_of_kwargs):
try:
return cls.add_all([
cls.new(**kwargs) if kwargs is not None else None for kwargs in list_of_kwargs])
except:
cls.session.rollback()
raise | 842,747 |
Similar to create. But the transaction is not committed
Args:
**kwargs : The keyword arguments for the constructor
Returns:
A model instance which has been added to db session. But session
transaction has not been committed yet. | def build(cls, **kwargs):
return cls.add(cls.new(**kwargs), commit=False) | 842,750 |
Checks if an instance already exists in db with these kwargs else
returns a new, saved instance of the service's model class.
Args:
**kwargs: instance parameters | def find_or_build(cls, **kwargs):
keys = kwargs.pop('keys') if 'keys' in kwargs else []
return cls.first(**subdict(kwargs, keys)) or cls.build(**kwargs) | 842,751 |
Batch method for updating all instances obeying the criterion
Args:
*criterion: SQLAlchemy query criterion for filtering what
instances to update
**kwargs: The parameters to be updated
Examples:
>>> User.update_all(active=True)
>>> Cust... | def update_all(cls, *criterion, **kwargs):
try:
r = cls.query.filter(*criterion).update(kwargs, 'fetch')
cls.session.commit()
return r
except:
cls.session.rollback()
raise | 842,756 |
Returns an updated instance of the service's model class.
Args:
model: the model to update
**kwargs: update parameters | def get_and_update(cls, id, **kwargs):
model = cls.get(id)
for k, v in cls._preprocess_params(kwargs).items():
setattr(model, k, v)
cls.session.commit()
return model | 842,757 |
Returns an updated instance of the service's model class.
Args:
model: the model to update
**kwargs: update parameters | def get_and_setattr(cls, id, **kwargs):
model = cls.get(id)
for k, v in cls._preprocess_params(kwargs).items():
setattr(model, k, v)
return model | 842,758 |
Create new_browser_window_is_opened object.
Args:
selenium:
(:py:class:`~selenium.webdriver.remote.webdriver.WebDriver`):
Firefox WebDriver object.
handles: (:obj:`list` of str): List of current Firefox window
handles. | def __init__(self, selenium, handles):
self.selenium = selenium
self.handles = handles | 842,847 |
Ask a question and get the input values.
This method will validade the input values.
Args:
field_name(string): Field name used to ask for input value.
pattern(tuple): Pattern to validate the input value.
is_required(bool): Boolean value if the input value is required... | def ask_question(self, field_name, pattern=NAME_PATTERN, is_required=False,
password=False):
input_value = ""
question = ("Insert the field using the pattern below:"
"\n{}\n{}: ".format(pattern[0], field_name))
while not input_value:
... | 842,869 |
Create a BaseWindow object.
Args:
selenium:
(:py:class:`~selenium.webdriver.remote.webdriver.WebDriver`):
Firefox WebDriver object.
handle: (str): WebDriver Firefox window handle. | def __init__(self, selenium, handle):
self.selenium = selenium
self.handle = handle
self.wait = WebDriverWait(self.selenium, timeout=10) | 842,872 |
Set info about NApp.
Args:
user (str): NApps Server username.
napp (str): NApp name.
version (str): NApp version. | def set_napp(self, user, napp, version=None):
self.user = user
self.napp = napp
self.version = version or 'latest' | 842,921 |
Get napp_dependencies from install NApp.
Args:
user(string) A Username.
napp(string): A NApp name.
Returns:
napps(list): List with tuples with Username and NApp name.
e.g. [('kytos'/'of_core'), ('kytos/of_l2ls')] | def dependencies(self, user=None, napp=None):
napps = self._get_napp_key('napp_dependencies', user, napp)
return [tuple(napp.split('/')) for napp in napps] | 842,924 |
Return a value from kytos.json.
Args:
user (string): A Username.
napp (string): A NApp name
key (string): Key used to get the value within kytos.json.
Returns:
meta (object): Value stored in kytos.json. | def _get_napp_key(self, key, user=None, napp=None):
if user is None:
user = self.user
if napp is None:
napp = self.napp
kytos_json = self._installed / user / napp / 'kytos.json'
try:
with kytos_json.open() as file_descriptor:
m... | 842,925 |
Search all server NApps matching pattern.
Args:
pattern (str): Python regular expression. | def search(pattern):
def match(napp):
# WARNING: This will change for future versions, when 'author' will
# be removed.
username = napp.get('username', napp.get('author'))
strings = ['{}/{}'.format(username, napp.get('name')),
... | 842,930 |
Return local NApp root folder.
Search for kytos.json in _./_ folder and _./user/napp_.
Args:
root (pathlib.Path): Where to begin searching.
Return:
pathlib.Path: NApp root folder.
Raises:
FileNotFoundError: If there is no such local NApp. | def _get_local_folder(self, root=None):
if root is None:
root = Path()
for folders in ['.'], [self.user, self.napp]:
kytos_json = root / Path(*folders) / 'kytos.json'
if kytos_json.exists():
with kytos_json.open() as file_descriptor:
... | 842,932 |
Create module folder with empty __init__.py if it doesn't exist.
Args:
folder (pathlib.Path): Module path. | def _check_module(folder):
if not folder.exists():
folder.mkdir(parents=True, exist_ok=True, mode=0o755)
(folder / '__init__.py').touch() | 842,938 |
Build the .napp file to be sent to the napps server.
Args:
napp_identifier (str): Identifier formatted as
<username>/<napp_name>
Return:
file_payload (binary): The binary representation of the napp
package that will be POSTed to the napp server. | def build_napp_package(napp_name):
ignored_extensions = ['.swp', '.pyc', '.napp']
ignored_dirs = ['__pycache__', '.git', '.tox']
files = os.listdir()
for filename in files:
if os.path.isfile(filename) and '.' in filename and \
filename.rsplit('.',... | 842,939 |
Reload a NApp or all NApps.
Args:
napps (list): NApp list to be reloaded.
Raises:
requests.HTTPError: When there's a server error. | def reload(self, napps=None):
client = NAppsClient(self._config)
client.reload_napps(napps) | 842,945 |
Create a Region object.
Args:
window (:py:class:`BaseWindow`): Window object this region appears
in.
root
(:py:class:`~selenium.webdriver.remote.webelement.WebElement`):
WebDriver element object that serves as the root for the
... | def __init__(self, window, root):
self.root = root
self.selenium = window.selenium
self.wait = window.wait
self.window = window | 843,118 |
Remove the pairs identified by the given indices into _pairs.
Removes the pair, and updates the _key_ids mapping to be accurate.
Removing the ids from the _key_ids is your own responsibility.
Params:
ids_to_remove -- The indices to remove. MUST be sorted. | def _remove_pairs(self, ids_to_remove):
# Remove them.
for i in reversed(ids_to_remove):
del self._pairs[i]
# We use the bisect to tell us how many spots the given index is
# shifting up in the list.
for ids in self._key_ids.itervalues():
... | 843,279 |
Insert some new pairs, and keep the _key_ids updated.
Params:
ids_and_pairs -- A list of (index, (key, value)) tuples. | def _insert_pairs(self, ids_and_pairs):
ids_to_insert = [x[0] for x in ids_and_pairs]
# We use the bisect to tell us how many spots the given index is
# shifting up in the list.
for ids in self._key_ids.itervalues():
for i, id in enumerate(ids):
... | 843,280 |
Wait for the specified notification to be displayed.
Args:
notification_class (:py:class:`BaseNotification`, optional):
The notification class to wait for. If `None` is specified it
will wait for any notification to be closed. Defaults to
`BaseNotific... | def wait_for_notification(self, notification_class=BaseNotification):
if notification_class:
if notification_class is BaseNotification:
message = "No notification was shown."
else:
message = "{0} was not shown.".format(notification_class.__name__)... | 843,326 |
Open a new browser window.
Args:
private (bool): Optional parameter to open a private browsing
window. Defaults to False.
Returns:
:py:class:`BrowserWindow`: Opened window. | def open_window(self, private=False):
handles_before = self.selenium.window_handles
self.switch_to()
with self.selenium.context(self.selenium.CONTEXT_CHROME):
# Opens private or non-private window
self.selenium.find_element(*self._file_menu_button_locator).click... | 843,328 |
Converts and instance to a dictionary with only the specified
attributes as keys
Args:
*args (list): The attributes to serialize
Examples:
>>> customer = Customer.create(name="James Bond", email="007@mi.com",
phone="007", city... | def serialize_attrs(self, *args):
# return dict([(a, getattr(self, a)) for a in args])
cls = type(self)
result = {}
# result = {
# a: getattr(self, a)
# for a in args
# if hasattr(cls, a) and
# a not in cls.attrs_forbidden_for_seri... | 843,346 |
Convert a napp_id in tuple with username, napp name and version.
Args:
napp_id: String with the form 'username/napp[:version]' (version is
optional). If no version is found, it will be None.
Returns:
tuple: A tuple with (username, napp, version)
Raises:
KytosExce... | def parse_napp(napp_id):
# `napp_id` regex, composed by two mandatory parts (username, napp_name)
# and one optional (version).
# username and napp_name need to start with a letter, are composed of
# letters, numbers and uderscores and must have at least three characters.
# They are separated b... | 843,352 |
Create FoxPuppet object.
Args:
selenium:
(:py:class:`~selenium.webdriver.remote.webdriver.WebDriver`):
Firefox WebDriver object. | def __init__(self, selenium):
self.selenium = selenium
self.window_manager = WindowManager(selenium)
# Need to ensure the first window is a browser window
self.browser = self.window_manager.windows[0] | 843,520 |
Renders a string from a path template using the provided bindings.
Args:
bindings (dict): A dictionary of var names to binding strings.
Returns:
str: The rendered instantiation of this path template.
Raises:
ValidationError: If a key isn't provided or if a ... | def render(self, bindings):
out = []
binding = False
for segment in self.segments:
if segment.kind == _BINDING:
if segment.literal not in bindings:
raise ValidationException(
('rendering error: value for key \'{}\' ... | 843,579 |
Matches a fully qualified path template string.
Args:
path (str): A fully qualified path template string.
Returns:
dict: Var names to matched binding values.
Raises:
ValidationException: If path can't be matched to the template. | def match(self, path):
this = self.segments
that = path.split('/')
current_var = None
bindings = {}
segment_count = self.segment_count
j = 0
for i in range(0, len(this)):
if j >= len(that):
break
if this[i].kind == ... | 843,580 |
Returns a list of path template segments parsed from data.
Args:
data: A path template string.
Returns:
A list of _Segment. | def parse(self, data):
self.binding_var_count = 0
self.segment_count = 0
segments = self.parser.parse(data)
# Validation step: checks that there are no nested bindings.
path_wildcard = False
for segment in segments:
if segment.kind == _TERMINAL and s... | 843,582 |
Create a notification object.
Args:
window (:py:class:`BrowserWindow`): Window object this region
appears in.
root
(:py:class:`~selenium.webdriver.remote.webelement.WebElement`):
WebDriver element object that serves as the root for the
... | def create(window, root):
notifications = {}
_id = root.get_property("id")
from foxpuppet.windows.browser.notifications import addons
notifications.update(addons.NOTIFICATIONS)
return notifications.get(_id, BaseNotification)(window, root) | 843,597 |
Instantiate an OpenAPI object.
Args:
napp_path (string): Napp directory
tlp_path (string): File name from template | def __init__(self, napp_path, tpl_path):
self._napp_path = napp_path
self._template = tpl_path / 'openapi.yml.template'
self._api_file = napp_path / 'openapi.yml'
metadata = napp_path / 'kytos.json'
self._napp = NApp.create_from_json(metadata)
# Data for a path... | 843,671 |
Gets to a certain marker position in the BED file.
Args:
n (int): The index of the marker to seek to. | def seek(self, n):
if self._mode != "r":
raise UnsupportedOperation("not available in 'w' mode")
if 0 <= n < self._nb_markers:
self._n = n
self._bed.seek(self._get_seek_position(n))
else:
# Invalid seek value
raise ValueError... | 843,806 |
Iterates over genotypes for a list of markers.
Args:
markers (list): The list of markers to iterate onto.
return_index (bool): Wether to return the marker's index or not.
Returns:
tuple: The name of the marker as a string, and its genotypes as a
:py:clas... | def iter_geno_marker(self, markers, return_index=False):
if self._mode != "r":
raise UnsupportedOperation("not available in 'w' mode")
# If string, we change to list
if isinstance(markers, str):
markers = [markers]
# Iterating over all markers
i... | 843,812 |
Iterates over genotypes for a list of markers (ACGT format).
Args:
markers (list): The list of markers to iterate onto.
Returns:
tuple: The name of the marker as a string, and its genotypes as a
:py:class:`numpy.ndarray` (ACGT format). | def iter_acgt_geno_marker(self, markers):
# We iterate over the markers
for snp, geno, s in self.iter_geno_marker(markers, return_index=True):
# Getting the SNP position and converting to ACGT
yield snp, self._allele_encoding[s][geno] | 843,813 |
Gets the genotypes for a given marker.
Args:
marker (str): The name of the marker.
return_index (bool): Wether to return the marker's index or not.
Returns:
numpy.ndarray: The genotypes of the marker (additive format). | def get_geno_marker(self, marker, return_index=False):
if self._mode != "r":
raise UnsupportedOperation("not available in 'w' mode")
# Check if the marker exists
if marker not in self._bim.index:
raise ValueError("{}: marker not in BIM".format(marker))
... | 843,814 |
Gets the genotypes for a given marker (ACGT format).
Args:
marker (str): The name of the marker.
Returns:
numpy.ndarray: The genotypes of the marker (ACGT format). | def get_acgt_geno_marker(self, marker):
# Getting the marker's genotypes
geno, snp_position = self.get_geno_marker(marker, return_index=True)
# Returning the ACGT's format of the genotypes
return self._allele_encoding[snp_position][geno] | 843,815 |
Write genotypes to binary file.
Args:
genotypes (numpy.ndarray): The genotypes to write in the BED file. | def write_genotypes(self, genotypes):
if self._mode != "w":
raise UnsupportedOperation("not available in 'r' mode")
# Initializing the number of samples if required
if self._nb_values is None:
self._nb_values = len(genotypes)
# Checking the expected num... | 843,816 |
Collect data into fixed-length chunks or blocks.
Args:
n (int): The size of the chunk.
fillvalue (int): The fill value.
Returns:
iterator: An iterator over the chunks. | def _grouper(iterable, n, fillvalue=0):
args = [iter(iterable)] * n
return zip_longest(fillvalue=fillvalue, *args) | 843,817 |
Retrieve the raster in the GRASS ASCII Grid format.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database.
Returns:
str: GRASS ASCII string. | def getAsGrassAsciiGrid(self, session):
if type(self.raster) != type(None):
# Make sure the raster field is valid
converter = RasterConverter(sqlAlchemyEngineOrSession=session)
return converter.getAsGrassAsciiRaster(tableName=self.tableName,
... | 843,909 |
Bulk ``register_item``.
Args:
items (iterable[Tree]):
Sequence of nodes to be registered as children. | def register_items(self, items):
for item in items:
item.set_parent(self)
self.items.extend(items) | 844,032 |
Fetch database for items matching.
Args:
page (int):
which page will be sliced
slice size is ``self.per_page``.
order_by (str):
a field name to order query by.
filters (dict):
a ``filter name``: ``value`` dict.
... | def get_items(self, page=1, order_by=None, filters=None):
start = (page-1)*self.per_page
query = self.get_query()
if order_by is not None:
query = query.order_by(self._get_field(order_by))
if filters is not None:
query = self._filter(query, filters)
... | 844,296 |
Retrieve the geometry in KML format.
This method is a veneer for an SQL query that calls the ``ST_AsKml()`` function on the geometry column.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database.
Returns:
str... | def getAsKml(self, session):
statement = .format(self.geometryColumnName,
self.tableName,
self.id)
result = session.execute(statement)
for row in result:
return row.kml | 844,489 |
Retrieve the geometry in Well Known Text format.
This method is a veneer for an SQL query that calls the ``ST_AsText()`` function on the geometry column.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database.
Returns:
... | def getAsWkt(self, session):
statement = .format(self.geometryColumnName,
self.tableName,
self.id)
result = session.execute(statement)
for row in result:
return row.wkt | 844,490 |
Retrieve the geometry in GeoJSON format.
This method is a veneer for an SQL query that calls the ``ST_AsGeoJSON()`` function on the geometry column.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database.
Returns:
... | def getAsGeoJson(self, session):
statement = .format(self.geometryColumnName,
self.tableName,
self.id)
result = session.execute(statement)
for row in result:
return row.json | 844,491 |
Retrieve the spatial reference id by which the geometry column is registered.
This method is a veneer for an SQL query that calls the ``ST_SRID()`` function on the geometry column.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled dat... | def getSpatialReferenceId(self, session):
statement = .format(self.geometryColumnName,
self.tableName,
self.id)
result = session.execute(statement)
for row in result:
return row.srid | 844,492 |
Append directory to relative paths in project file. By default, the project file paths are read and written as
relative paths. Use this method to prepend a directory to all the paths in the project file.
Args:
directory (str): Directory path to prepend to file paths in project file.
... | def appendDirectory(self, directory, projectFilePath):
lines = []
with open(projectFilePath, 'r') as original:
for l in original:
lines.append(l)
with open(projectFilePath, 'w') as new:
for line in lines:
card = {}
... | 844,634 |
Retrieve card object for given card name.
Args:
name (str): Name of card to be retrieved.
Returns:
:class:`.ProjectCard` or None: Project card object. Will return None if the card is not available. | def getCard(self, name):
cards = self.projectCards
for card in cards:
if card.name.upper() == name.upper():
return card
return None | 844,646 |
Adds/updates card for gssha project file
Args:
name (str): Name of card to be updated/added.
value (str): Value to attach to the card.
add_quotes (Optional[bool]): If True, will add quotes around string. Default is False. | def setCard(self, name, value, add_quotes=False):
gssha_card = self.getCard(name)
if add_quotes:
value = '"{0}"'.format(value)
if gssha_card is None:
# add new card
new_card = ProjectCard(name=name, value=value)
new_card.projectFile = se... | 844,647 |
Retrieve a Well Known Text representation of the model. Includes polygonized mask map and vector stream network.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database
withStreamNetwork (bool, optional): Include stream network.... | def getModelSummaryAsWkt(self, session, withStreamNetwork=True, withNodes=False):
# Get mask map
watershedMaskCard = self.getCard('WATERSHED_MASK')
maskFilename = watershedMaskCard.value
maskExtension = maskFilename.strip('"').split('.')[1]
maskMap = session.query(Raste... | 844,650 |
Retrieve a GeoJSON representation of the model. Includes vectorized mask map and stream network.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database
withStreamNetwork (bool, optional): Include stream network. Defaults to Tru... | def getModelSummaryAsGeoJson(self, session, withStreamNetwork=True, withNodes=False):
# Get mask map
watershedMaskCard = self.getCard('WATERSHED_MASK')
maskFilename = watershedMaskCard.value
maskExtension = maskFilename.strip('"').split('.')[1]
maskMap = session.query(R... | 844,651 |
Sets the outlet grid cell information in the project file.
Parameters:
col(float): 1-based column index.
row(float): 1-based row index.
outslope(Optional[float]): River slope at outlet. | def setOutlet(self, col, row, outslope=None):
#OUTROW, OUTCOL, OUTSLOPE
gssha_grid = self.getGrid()
# col, row = gssha_grid.lonlat2pixel(longitude, latitude)
# add 1 to row & col becasue GSSHA is 1-based
self.setCard(name='OUTROW', value=str(row))
self.setCard(na... | 844,657 |
Write project card to string.
Args:
originalPrefix (str): Original name to give to files that follow the project naming convention
(e.g: prefix.gag).
newPrefix (str, optional): If new prefix is desired, pass in this parameter. Defaults to None.
Returns:
... | def write(self, originalPrefix, newPrefix=None):
# Determine number of spaces between card and value for nice alignment
numSpaces = max(2, 25 - len(self.name))
# Handle special case of booleans
if self.value is None:
line = '%s\n' % self.name
else:
... | 844,679 |
Look up spatial reference system using the projection file.
Args:
directory (str):
filename (str):
Return:
int: Spatial Reference ID | def lookupSpatialReferenceID(cls, directory, filename):
path = os.path.join(directory, filename)
with open(path, 'r') as f:
srid = lookupSpatialReferenceID(f.read())
return srid | 844,853 |
Log events to the console.
Args:
status (bool, Optional, Default=True)
whether logging to console should be turned on(True) or off(False)
level (string, Optional, Default=None) :
level of logging; whichever level is chosen all higher levels will be logged.
See: ... | def log_to_console(status=True, level=None):
if status:
if level is not None:
logger.setLevel(level)
console_handler = logging.StreamHandler()
# create formatter
formatter = logging.Formatter('%(levelname)s-%(name)s: %(message)s')
# add formatter to handler... | 844,856 |
Log events to a file.
Args:
status (bool, Optional, Default=True)
whether logging to file should be turned on(True) or off(False)
filename (string, Optional, Default=None) :
path of file to log to
level (string, Optional, Default=None) :
level of logging;... | def log_to_file(status=True, filename=default_log_file, level=None):
if status:
if level is not None:
logger.setLevel(level)
try:
os.mkdir(os.path.dirname(filename))
except OSError:
pass
file_handler = logging.FileHandler(filename)
... | 844,857 |
Apply global pre-processing to values during reading throughout the project.
Args:
valueString (str): String representing the value to be preprocessed.
replaceParamsFile (gsshapy.orm.ReplaceParamFile, optional): Instance of the replace param file. Required if
replacement variables are i... | def valueReadPreprocessor(valueString, replaceParamsFile=None):
if type(valueString) is bool:
log.warning("Only numerical variable types can be handled by the valueReadPreprocessor function.")
return valueString
# Default
processedValue = valueString
# Check for replacement variab... | 844,943 |
Look up variable name in replace param file for the negative id given and return it.
Args:
valueString (str): String representing the value to be preprocessed.
replaceParamsFile (gsshapy.orm.ReplaceParamFile, optional): Instance of the replace param file. Required if
replacement variabl... | def valueWritePreprocessor(valueString, replaceParamsFile=None):
if type(valueString) is bool:
log.warning("Only numerical variable types can be handled by the valueReadPreprocessor function.")
return valueString
# Default
variableString = valueString
# Check for replacement varia... | 844,944 |
Executes all the tests for pyplink.
Args:
verbosity (int): The verbosity level for :py:mod:`unittest`.
Just set ``verbosity`` to an integer higher than ``1`` to have more
information about the tests. | def test(verbosity=1): # pragma: no cover
import unittest
from .tests import test_suite
# Testing
unittest.TextTestRunner(verbosity=verbosity).run(test_suite) | 845,187 |
Retrieve the links in the order of the link number.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database.
Returns:
list: A list of :class:`.StreamLink` objects. | def getOrderedLinks(self, session):
streamLinks = session.query(StreamLink).\
filter(StreamLink.channelInputFile == self).\
order_by(StreamLink.linkNumber).\
all()
return streamLinks | 845,345 |
Retrieve the stream network geometry in Well Known Text format.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database
withNodes (bool, optional): Include nodes. Defaults to False.
Returns:
str: Well Known ... | def getStreamNetworkAsWkt(self, session, withNodes=True):
wkt_list = []
for link in self.streamLinks:
wkt_link = link.getAsWkt(session)
if wkt_link:
wkt_list.append(wkt_link)
if withNodes:
for node in link.nodes:
... | 845,347 |
Retrieve the stream network geometry in GeoJSON format.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database
withNodes (bool, optional): Include nodes. Defaults to False.
Returns:
str: GeoJSON string. | def getStreamNetworkAsGeoJson(self, session, withNodes=True):
features_list = []
# Assemble link features
for link in self.streamLinks:
link_geoJson = link.getAsGeoJson(session)
if link_geoJson:
link_geometry = json.loads(link.getAsGeoJson(sessi... | 845,348 |
A Basic View with template.
Args:
view_name (str): The name of the view,
used to create a custom template name.
success_url (str): The url returned by ``post`` if form is valid. | def __init__(self, view_name, success_url=None):
if success_url is not None:
self.success_url = success_url
self.view_name = view_name | 845,455 |
A simple landing view, template may be overwriten to customize.
Args:
parent (Group): ``Group`` host of ``self``. | def __init__(self, parent, *args, **kwargs):
self.parent = parent
super().__init__(*args, **kwargs) | 845,457 |
Concat Urls
Args:
*args: (str)
Returns:
str: urls starting and ending with / merged with / | def concat_urls(*urls):
normalized_urls = filter(bool, [url.strip('/') for url in urls])
joined_urls = '/'.join(normalized_urls)
if not joined_urls:
return '/'
return '/{}/'.format(joined_urls) | 845,468 |
Add the genes for a variant
Get the hgnc symbols from all transcripts and add them
to the variant.
Args:
variant (dict): A variant dictionary
Returns:
genes (list): A list of Genes | def _get_genes(self, variant):
transcripts = variant['transcripts']
ensembl_ids = [transcript['ensembl_id'] for transcript in
transcripts if transcript['ensembl_id']]
hgnc_symbols = [transcript['hgnc_symbol'] for transcript in
transcripts i... | 845,511 |
Authenticate the gmusicapi Mobileclient instance.
Parameters:
username (Optional[str]): Your Google Music username. Will be prompted if not given.
password (Optional[str]): Your Google Music password. Will be prompted if not given.
android_id (Optional[str]): The 16 hex digits from an Android device ID.
... | def login(self, username=None, password=None, android_id=None):
cls_name = type(self).__name__
if username is None:
username = input("Enter your Google username or email address: ")
if password is None:
password = getpass.getpass("Enter your Google Music password: ")
if android_id is None:
andro... | 845,519 |
Get playlist information of a user-generated Google Music playlist.
Parameters:
playlist (str): Name or ID of Google Music playlist. Names are case-sensitive.
Google allows multiple playlists with the same name.
If multiple playlists have the same name, the first one encountered is used.
Returns:
di... | def get_google_playlist(self, playlist):
logger.info("Loading playlist {0}".format(playlist))
for google_playlist in self.api.get_all_user_playlist_contents():
if google_playlist['name'] == playlist or google_playlist['id'] == playlist:
return google_playlist
else:
logger.warning("Playlist {0} does... | 845,521 |
Load a case with individuals.
Args:
case_obj (puzzle.models.Case): initialized case model | def add_case(self, case_obj, vtype='snv', mode='vcf', ped_svg=None):
new_case = Case(case_id=case_obj.case_id,
name=case_obj.name,
variant_source=case_obj.variant_source,
variant_type=vtype,
variant_mode=mod... | 845,531 |
Delete a case from the database
Args:
case_obj (puzzle.models.Case): initialized case model | def delete_case(self, case_obj):
for ind_obj in case_obj.individuals:
self.delete_individual(ind_obj)
logger.info("Deleting case {0} from database".format(case_obj.case_id))
self.session.delete(case_obj)
self.save()
return case_obj | 845,532 |
Delete a case from the database
Args:
ind_obj (puzzle.models.Individual): initialized individual model | def delete_individual(self, ind_obj):
logger.info("Deleting individual {0} from database"
.format(ind_obj.ind_id))
self.session.delete(ind_obj)
self.save()
return ind_obj | 845,533 |
Add the thousand genomes frequency
Args:
variant_obj (puzzle.models.Variant)
info_dict (dict): A info dictionary | def _add_thousand_g(self, variant_obj, info_dict):
thousand_g = info_dict.get('1000GAF')
if thousand_g:
logger.debug("Updating thousand_g to: {0}".format(
thousand_g))
variant_obj.thousand_g = float(thousand_g)
variant_obj.add_frequency('1000G... | 845,629 |
Add the gmaf frequency
Args:
variant_obj (puzzle.models.Variant)
info_dict (dict): A info dictionary | def _add_gmaf(self, variant_obj, info_dict):
##TODO search for max freq in info dict
for transcript in variant_obj.transcripts:
gmaf_raw = transcript.GMAF
if gmaf_raw:
gmaf = float(gmaf_raw.split(':')[-1])
variant_obj.add_frequency('GMAF',... | 845,630 |
Add the gmaf frequency
Args:
variant_obj (puzzle.models.Variant)
info_dict (dict): A info dictionary | def _add_exac(self, variant_obj, info_dict):
exac = None
exac_keys = ['ExAC', 'EXAC', 'ExACAF', 'EXACAF']
for key in exac_keys:
if info_dict.get(key):
exac = float(info_dict[key])
#If not found in vcf search transcripts
if not exac:
... | 845,631 |
Add the genotypes for a variant for all individuals
Args:
variant_obj (puzzle.models.Variant)
gemini_variant (GeminiQueryRow): The gemini variant
case_id (str): related case id
individual_objs (list(dict)): A list of Indivi... | def _add_genotypes(self, variant_obj, gemini_variant, case_id,
individual_objs):
for ind in individual_objs:
index = ind.ind_index
variant_obj.add_individual(Genotype(
sample_id=ind.ind_id,
genotype=gemini_variant['gts'][ind... | 845,641 |
Recognizes and claims MuTect VCFs form the set of all input VCFs.
Each defined caller has a chance to evaluate and claim all the incoming
files as something that it can process.
Args:
file_readers: the collection of currently unclaimed files
Returns:
A tuple of... | def claim(self, file_readers):
unclaimed_readers = []
vcf_readers = []
for file_reader in file_readers:
if self._is_mutect_vcf(file_reader):
vcf_reader = vcf.VcfReader(file_reader)
vcf_readers.append(_MutectVcfReader(vcf_reader))
e... | 845,658 |
Add the gmaf frequency
Args:
variant_obj (puzzle.models.Variant)
gemini_variant (GeminiQueryRow) | def _add_gmaf(self, variant_obj, gemini_variant):
max_af = gemini_variant['max_aaf_all']
if max_af:
max_af = float(max_af)
if max_af != -1.0:
variant_obj.set_max_freq(max_af) | 845,708 |
Add the gmaf frequency
Args:
variant_obj (puzzle.models.Variant)
gemini_variant (GeminiQueryRow) | def _add_exac(self, variant_obj, gemini_variant):
exac = gemini_variant['aaf_exac_all']
if exac:
exac = float(exac)
variant_obj.add_frequency('ExAC', exac)
logger.debug("Updating ExAC to: {0}".format(
exac)) | 845,709 |
Return the genes info based on the transcripts found
Args:
ensembl_ids (Optional[list]): list of Ensembl gene ids
hgnc_symbols (Optional[list]): list of HGNC gene symbols
Returns:
iterable: an iterable with `Gene` objects | def get_gene_info(ensembl_ids=None, hgnc_symbols=None):
uniq_ensembl_ids = set(ensembl_id for ensembl_id in (ensembl_ids or []))
uniq_hgnc_symbols = set(hgnc_symbol for hgnc_symbol in (hgnc_symbols or []))
genes = []
gene_data = []
if uniq_ensembl_ids:
for ensembl_id in uniq_ensemb... | 845,712 |
Get the most severe consequence
Go through all transcripts and get the most severe consequence
Args:
transcripts (list): A list of transcripts to evaluate
Returns:
most_severe_consequence (str): The most severe consequence | def get_most_severe_consequence(transcripts):
most_severe_consequence = None
most_severe_score = None
for transcript in transcripts:
for consequence in transcript['consequence'].split('&'):
logger.debug("Checking severity score for consequence: {0}".format(
conseque... | 845,713 |
Get the cytoband coordinate for a position
Args:
chrom(str): A chromosome
pos(int): The position
Returns:
cytoband | def get_cytoband_coord(chrom, pos):
chrom = chrom.strip('chr')
pos = int(pos)
result = None
logger.debug("Finding Cytoband for chrom:{0} pos:{1}".format(chrom, pos))
if chrom in CYTOBANDS:
for interval in CYTOBANDS[chrom][pos]:
result = "{0}{1}".format(chrom, interval.data)
... | 845,714 |
Create a cases and populate it with individuals
Args:
variant_source (str): Path to vcf files
case_lines (Iterable): Ped like lines
case_type (str): Format of case lines
Returns:
case_objs (list(puzzle.models.Case)) | def get_cases(variant_source, case_lines=None, case_type='ped',
variant_type='snv', variant_mode='vcf'):
individuals = get_individuals(
variant_source=variant_source,
case_lines=case_lines,
case_type=case_type,
variant_mode=variant_mode
... | 845,743 |
Get the individuals from a vcf file, gemini database, and/or a ped file.
Args:
variant_source (str): Path to a variant source
case_lines(Iterable): Ped like lines
case_type(str): Format of ped lines
Returns:
individuals (generator... | def get_individuals(variant_source, case_lines=None, case_type='ped', variant_mode='vcf'):
individuals = []
ind_dict ={}
if variant_mode == 'vcf':
head = get_header(variant_source)
#Dictionary with ind_id:index where index show where in vcf ind info is
... | 845,744 |
Add the cadd score to the variant
Args:
variant_obj (puzzle.models.Variant)
info_dict (dict): A info dictionary | def _add_cadd_score(self, variant_obj, info_dict):
cadd_score = info_dict.get('CADD')
if cadd_score:
logger.debug("Updating cadd_score to: {0}".format(
cadd_score))
variant_obj.cadd_score = float(cadd_score) | 845,754 |
Add the genetic models found
Args:
variant_obj (puzzle.models.Variant)
info_dict (dict): A info dictionary | def _add_genetic_models(self, variant_obj, info_dict):
genetic_models_entry = info_dict.get('GeneticModels')
if genetic_models_entry:
genetic_models = []
for family_annotation in genetic_models_entry.split(','):
for genetic_model in family_annotation.spli... | 845,755 |
Add the rank score if found
Args:
variant_obj (puzzle.models.Variant)
info_dict (dict): A info dictionary | def _add_rank_score(self, variant_obj, info_dict):
rank_score_entry = info_dict.get('RankScore')
if rank_score_entry:
for family_annotation in rank_score_entry.split(','):
rank_score = family_annotation.split(':')[-1]
logger.debug("Updating rank_score to:... | 845,756 |
Configure connection to a SQL database.
Args:
db_uri (str): path/URI to the database to connect to
debug (Optional[bool]): whether to output logging information | def connect(self, db_uri, debug=False):
kwargs = {'echo': debug, 'convert_unicode': True}
# connect to the SQL database
if 'mysql' in db_uri:
kwargs['pool_recycle'] = 3600
elif '://' not in db_uri:
logger.debug("detected sqlite path URI: {}".format(db_uri... | 845,766 |
Parsers a file or string and returns a list of AudioClipSpec
Arguments:
specsFileOrString (str): specifications' file or string
Examples:
>>> SpecsParser.parse('23.4 34.1\n40.2 79.65 Hello World!')
[<AudioClipSpec start:23.40, end:34.10, text:''>,
... | def parse(cls, specsFileOrString):
stringToParse = None
# Read the contents of the file if specsFileOrString is not a string
if os.path.isfile(specsFileOrString):
with open(specsFileOrString, 'r') as f:
stringToParse = f.read()
else:
stri... | 845,835 |
Return comments for a case or variant.
Args:
case_id (str): id for a related case
variant_id (Optional[str]): id for a related variant | def comments(self, case_id=None, variant_id=None, username=None):
logger.debug("Looking for comments")
comment_objs = self.query(Comment)
if case_id:
comment_objs = comment_objs.filter_by(case_id=case_id)
if variant_id:
comment_objs = comment_objs.filte... | 845,919 |
Add the consequences found for a variant
Args:
variant_obj (puzzle.models.Variant)
raw_variant_line (str): A raw vcf variant line | def _add_consequences(self, variant_obj, raw_variant_line):
consequences = []
for consequence in SO_TERMS:
if consequence in raw_variant_line:
consequences.append(consequence)
variant_obj.consequences = consequences | 845,922 |
Add the most severe consequence
Args:
variant_obj (puzzle.models.Variant) | def _add_most_severe_consequence(self, variant_obj):
most_severe_consequence = None
most_severe_score = None
for consequence in variant_obj.consequences:
logger.debug("Checking severity score for consequence: {0}".format(
consequence))
... | 845,923 |
Add the impact severity for the most severe consequence
Args:
variant_obj (puzzle.models.Variant) | def _add_impact_severity(self, variant_obj):
if variant_obj.most_severe_consequence:
variant_obj.impact_severity = IMPACT_SEVERITIES.get(
variant_obj.most_severe_consequence
) | 845,924 |
Add a individual to the adapter
Args:
ind_obj (puzzle.models.Individual) | def _add_individual(self, ind_obj):
logger.debug("Adding individual {0} to plugin".format(ind_obj.ind_id))
self.individual_objs.append(ind_obj) | 846,151 |
Add a case obj with individuals to adapter
Args:
case_obj (puzzle.models.Case) | def add_case(self, case_obj):
for ind_obj in case_obj.individuals:
self._add_individual(ind_obj)
logger.debug("Adding case {0} to plugin".format(case_obj.case_id))
self.case_objs.append(case_obj) | 846,152 |
Return a Case object
If no case_id is given return one case
Args:
case_id (str): A case id
Returns:
case(Case): A Case object | def case(self, case_id=None):
cases = self.cases()
if case_id:
for case in cases:
if case.case_id == case_id:
return case
else:
if cases:
return cases[0]
return None | 846,153 |
Return a individual object
Args:
ind_id (str): A individual id
Returns:
individual (puzzle.models.individual) | def individual(self, ind_id=None):
for ind_obj in self.individuals:
if ind_obj.ind_id == ind_id:
return ind_obj
return None | 846,154 |
Allows each caller to claim incoming files as they are recognized.
Args:
unclaimed_file_readers: Usually, all files in the input dir.
Returns:
A tuple of unclaimed file readers and claimed VcfReaders. The
presence of any unclaimed file readers could indicate stray f... | def claim(self, unclaimed_file_readers):
claimed_vcf_readers = []
for caller in self._callers:
(unclaimed_file_readers,
translated_vcf_readers) = caller.claim(unclaimed_file_readers)
claimed_vcf_readers.extend(translated_vcf_readers)
return unclaime... | 846,252 |
Flask app factory function.
Args:
config (Optional[path]): path to a Python module config file
config_obj (Optional[class]): Python config object | def create_app(config=None, config_obj=None):
app = Flask(__name__)
# configure application from external configs
configure_app(app, config=config, config_obj=config_obj)
# register different parts of the application
register_blueprints(app)
# setup extensions
bind_extensions(app)
r... | 846,315 |
Configure application instance.
Args:
app (Flask): initialized Flask app instance
config (Optional[path]): path to a Python module config file
config_obj (Optional[class]): Python config object | def configure_app(app, config=None, config_obj=None):
app.config.from_object(config_obj or BaseConfig)
if config is not None:
app.config.from_pyfile(config) | 846,316 |
Configure extensions.
Args:
app (Flask): initialized Flask app instance | def bind_extensions(app):
# bind plugin to app object
app.db = app.config['PUZZLE_BACKEND']
app.db.init_app(app)
# bind bootstrap blueprints
bootstrap.init_app(app)
markdown(app)
@app.template_filter('islist')
def islist(object):
return isinstance(object, (tuple, list)) | 846,317 |
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