sentence1 stringlengths 52 3.87M | sentence2 stringlengths 1 47.2k | label stringclasses 1
value |
|---|---|---|
def get_logs(self, login=None, **kwargs):
"""Get a user's logs.
:param str login: User's login (Default: self._login)
:return: JSON
"""
_login = kwargs.get(
'login',
login
)
log_events_url = GSA_LOGS_URL.format(login=_login)
retur... | Get a user's logs.
:param str login: User's login (Default: self._login)
:return: JSON | entailment |
def negotiate(cls, headers):
""" Process headers dict to return the format class
(not the instance)
"""
# set lower keys
headers = {k.lower(): v for k, v in headers.items()}
accept = headers.get('accept', "*/*")
parsed_accept = accept.split(";")
pars... | Process headers dict to return the format class
(not the instance) | entailment |
def register(self, collector):
""" Registers a collector"""
if not isinstance(collector, Collector):
raise TypeError(
"Can't register instance, not a valid type of collector")
if collector.name in self.collectors:
raise ValueError("Collector already exist... | Registers a collector | entailment |
def add(self, registry):
""" Add works like replace, but only previously pushed metrics with the
same name (and the same job and instance) will be replaced.
(It uses HTTP method 'POST' to push to the Pushgateway.)
"""
# POST
payload = self.formatter.marshall(regis... | Add works like replace, but only previously pushed metrics with the
same name (and the same job and instance) will be replaced.
(It uses HTTP method 'POST' to push to the Pushgateway.) | entailment |
def replace(self, registry):
""" Push triggers a metric collection and pushes all collected metrics
to the Pushgateway specified by addr
Note that all previously pushed metrics with the same job and
instance will be replaced with the metrics pushed by this call.
(... | Push triggers a metric collection and pushes all collected metrics
to the Pushgateway specified by addr
Note that all previously pushed metrics with the same job and
instance will be replaced with the metrics pushed by this call.
(It uses HTTP method 'PUT' to push to the ... | entailment |
def marshall_lines(self, collector):
""" Marshalls a collector and returns the storage/transfer format in
a tuple, this tuple has reprensentation format per element.
"""
if isinstance(collector, collectors.Counter):
exec_method = self._format_counter
elif isinsta... | Marshalls a collector and returns the storage/transfer format in
a tuple, this tuple has reprensentation format per element. | entailment |
def marshall(self, registry):
"""Marshalls a full registry (various collectors)"""
blocks = []
for i in registry.get_all():
blocks.append(self.marshall_collector(i))
# Sort? used in tests
blocks = sorted(blocks)
# Needs EOF
blocks.append("")
... | Marshalls a full registry (various collectors) | entailment |
def marshall(self, registry):
"""Returns bytes"""
result = b""
for i in registry.get_all():
# Each message needs to be prefixed with a varint with the size of
# the message (MetrycType)
# https://github.com/matttproud/golang_protobuf_extensions/blob/master/ex... | Returns bytes | entailment |
def gather_data(registry):
"""Gathers the metrics"""
# Get the host name of the machine
host = socket.gethostname()
# Create our collectors
trig_metric = Gauge("trigonometry_example",
"Various trigonometry examples.",
{'host': host})
# register ... | Gathers the metrics | entailment |
def set_value(self, labels, value):
""" Sets a value in the container"""
if labels:
self._label_names_correct(labels)
with mutex:
self.values[labels] = value | Sets a value in the container | entailment |
def _label_names_correct(self, labels):
"""Raise exception (ValueError) if labels not correct"""
for k, v in labels.items():
# Check reserved labels
if k in RESTRICTED_LABELS_NAMES:
raise ValueError("Labels not correct")
# Check prefixes
... | Raise exception (ValueError) if labels not correct | entailment |
def get_all(self):
""" Returns a list populated by tuples of 2 elements, first one is
a dict with all the labels and the second elemnt is the value
of the metric itself
"""
with mutex:
items = self.values.items()
result = []
for k, v in items:... | Returns a list populated by tuples of 2 elements, first one is
a dict with all the labels and the second elemnt is the value
of the metric itself | entailment |
def add(self, labels, value):
""" Add adds the given value to the Gauge. (The value can be
negative, resulting in a decrease of the Gauge.)
"""
try:
current = self.get_value(labels)
except KeyError:
current = 0
self.set_value(labels, current ... | Add adds the given value to the Gauge. (The value can be
negative, resulting in a decrease of the Gauge.) | entailment |
def add(self, labels, value):
"""Add adds a single observation to the summary."""
if type(value) not in (float, int):
raise TypeError("Summary only works with digits (int, float)")
# We have already a lock for data but not for the estimator
with mutex:
try:
... | Add adds a single observation to the summary. | entailment |
def get(self, labels):
""" Get gets the data in the form of 0.5, 0.9 and 0.99 percentiles. Also
you get sum and count, all in a dict
"""
return_data = {}
# We have already a lock for data but not for the estimator
with mutex:
e = self.get_value(labels)
... | Get gets the data in the form of 0.5, 0.9 and 0.99 percentiles. Also
you get sum and count, all in a dict | entailment |
def gather_data(registry):
"""Gathers the metrics"""
# Get the host name of the machine
host = socket.gethostname()
# Create our collectors
ram_metric = Gauge("memory_usage_bytes", "Memory usage in bytes.",
{'host': host})
cpu_metric = Gauge("cpu_usage_percent", "CPU usa... | Gathers the metrics | entailment |
def gather_data(registry):
"""Gathers the metrics"""
# Get the host name of the machine
host = socket.gethostname()
# Create our collectors
io_metric = Summary("write_file_io_example",
"Writing io file in disk example.",
{'host': host})
# regist... | Gathers the metrics | entailment |
def get_child(self, name, attribs=None):
"""
Returns the first child that matches the given name and
attributes.
"""
if name == '.':
if attribs is None or len(attribs) == 0:
return self
if attribs == self.attribs:
return sel... | Returns the first child that matches the given name and
attributes. | entailment |
def create(self, path, data=None):
"""
Creates the given node, regardless of whether or not it already
exists.
Returns the new node.
"""
node = self.current[-1]
path = self._splitpath(path)
n_items = len(path)
for n, item in enumerate(path):
... | Creates the given node, regardless of whether or not it already
exists.
Returns the new node. | entailment |
def add(self, path, data=None, replace=False):
"""
Creates the given node if it does not exist.
Returns the (new or existing) node.
"""
node = self.current[-1]
for item in self._splitpath(path):
tag, attribs = self._splittag(item)
next_node = node.... | Creates the given node if it does not exist.
Returns the (new or existing) node. | entailment |
def add_attribute(self, path, name, value):
"""
Creates the given attribute and sets it to the given value.
Returns the (new or existing) node to which the attribute was added.
"""
node = self.add(path)
node.attribs.append((name, value))
return node | Creates the given attribute and sets it to the given value.
Returns the (new or existing) node to which the attribute was added. | entailment |
def open(self, path):
"""
Creates and enters the given node, regardless of whether it already
exists.
Returns the new node.
"""
self.current.append(self.create(path))
return self.current[-1] | Creates and enters the given node, regardless of whether it already
exists.
Returns the new node. | entailment |
def enter(self, path):
"""
Enters the given node. Creates it if it does not exist.
Returns the node.
"""
self.current.append(self.add(path))
return self.current[-1] | Enters the given node. Creates it if it does not exist.
Returns the node. | entailment |
def generate(converter, input_file, format='xml', encoding='utf8'):
"""
Given a converter (as returned by compile()), this function reads
the given input file and converts it to the requested output format.
Supported output formats are 'xml', 'yaml', 'json', or 'none'.
:type converter: compiler.C... | Given a converter (as returned by compile()), this function reads
the given input file and converts it to the requested output format.
Supported output formats are 'xml', 'yaml', 'json', or 'none'.
:type converter: compiler.Context
:param converter: The compiled converter.
:type input_file: str
... | entailment |
def generate_to_file(converter,
input_file,
output_file,
format='xml',
in_encoding='utf8',
out_encoding='utf8'):
"""
Like generate(), but writes the output to the given output file
instead.
:type c... | Like generate(), but writes the output to the given output file
instead.
:type converter: compiler.Context
:param converter: The compiled converter.
:type input_file: str
:param input_file: Name of a file to convert.
:type output_file: str
:param output_file: The output filename.
:ty... | entailment |
def generate_string(converter, input, format='xml'):
"""
Like generate(), but reads the input from a string instead of
from a file.
:type converter: compiler.Context
:param converter: The compiled converter.
:type input: str
:param input: The string to convert.
:type format: str
... | Like generate(), but reads the input from a string instead of
from a file.
:type converter: compiler.Context
:param converter: The compiled converter.
:type input: str
:param input: The string to convert.
:type format: str
:param format: The output format.
:rtype: str
:return: T... | entailment |
def generate_string_to_file(converter,
input,
output_file,
format='xml',
out_encoding='utf8'):
"""
Like generate(), but reads the input from a string instead of
from a file, and writes the output ... | Like generate(), but reads the input from a string instead of
from a file, and writes the output to the given output file.
:type converter: compiler.Context
:param converter: The compiled converter.
:type input: str
:param input: The string to convert.
:type output_file: str
:param outpu... | entailment |
def is_now(s, dt=None):
'''
A very simple cron-like parser to determine, if (cron-like) string is valid for this date and time.
@input:
s = cron-like string (minute, hour, day of month, month, day of week)
dt = datetime to use as reference time, defaults to now
@output: boolean of result... | A very simple cron-like parser to determine, if (cron-like) string is valid for this date and time.
@input:
s = cron-like string (minute, hour, day of month, month, day of week)
dt = datetime to use as reference time, defaults to now
@output: boolean of result | entailment |
def has_been(s, since, dt=None):
'''
A parser to check whether a (cron-like) string has been true during a certain time period.
Useful for applications which cannot check every minute or need to catch up during a restart.
@input:
s = cron-like string (minute, hour, day of month, month, day of we... | A parser to check whether a (cron-like) string has been true during a certain time period.
Useful for applications which cannot check every minute or need to catch up during a restart.
@input:
s = cron-like string (minute, hour, day of month, month, day of week)
since = datetime to use as refere... | entailment |
def auprc(y_true, y_pred):
"""Area under the precision-recall curve
"""
y_true, y_pred = _mask_value_nan(y_true, y_pred)
return skm.average_precision_score(y_true, y_pred) | Area under the precision-recall curve | entailment |
def best_trial_tid(self, rank=0):
"""Get tid of the best trial
rank=0 means the best model
rank=1 means second best
...
"""
candidates = [t for t in self.trials
if t['result']['status'] == STATUS_OK]
if len(candidates) == 0:
retu... | Get tid of the best trial
rank=0 means the best model
rank=1 means second best
... | entailment |
def count_by_state_unsynced(self, arg):
"""Extends the original object in order to inject checking
for stalled jobs and killing them if they are running for too long
"""
if self.kill_timeout is not None:
self.delete_running(self.kill_timeout)
return super(KMongoTrials... | Extends the original object in order to inject checking
for stalled jobs and killing them if they are running for too long | entailment |
def plot_history(self, tid, scores=["loss", "f1", "accuracy"],
figsize=(15, 3)):
"""Plot the loss curves"""
history = self.train_history(tid)
import matplotlib.pyplot as plt
fig = plt.figure(figsize=figsize)
for i, score in enumerate(scores):
plt... | Plot the loss curves | entailment |
def load_model(self, tid, custom_objects=None):
"""Load saved keras model of the trial.
If tid = None, get the best model
Not applicable for trials ran in cross validion (i.e. not applicable
for `CompileFN.cv_n_folds is None`
"""
if tid is None:
tid = self.b... | Load saved keras model of the trial.
If tid = None, get the best model
Not applicable for trials ran in cross validion (i.e. not applicable
for `CompileFN.cv_n_folds is None` | entailment |
def n_ok(self):
"""Number of ok trials()
"""
if len(self.trials) == 0:
return 0
else:
return np.sum(np.array(self.statuses()) == "ok") | Number of ok trials() | entailment |
def get_ok_results(self, verbose=True):
"""Return a list of results with ok status
"""
if len(self.trials) == 0:
return []
not_ok = np.where(np.array(self.statuses()) != "ok")[0]
if len(not_ok) > 0 and verbose:
print("{0}/{1} trials were not ok.".format(... | Return a list of results with ok status | entailment |
def VerifierMiddleware(verifier):
"""Common wrapper for the authentication modules.
* Parses the request before passing it on to the authentication module.
* Sets 'pyoidc' cookie if authentication succeeds.
* Redirects the user to complete the authentication.
* Allows the user to ret... | Common wrapper for the authentication modules.
* Parses the request before passing it on to the authentication module.
* Sets 'pyoidc' cookie if authentication succeeds.
* Redirects the user to complete the authentication.
* Allows the user to retry authentication if it fails.
:param... | entailment |
def pyoidcMiddleware(func):
"""Common wrapper for the underlying pyoidc library functions.
Reads GET params and POST data before passing it on the library and
converts the response from oic.utils.http_util to wsgi.
:param func: underlying library function
"""
def wrapper(environ, start_response... | Common wrapper for the underlying pyoidc library functions.
Reads GET params and POST data before passing it on the library and
converts the response from oic.utils.http_util to wsgi.
:param func: underlying library function | entailment |
def resp2flask(resp):
"""Convert an oic.utils.http_util instance to Flask."""
if isinstance(resp, Redirect) or isinstance(resp, SeeOther):
code = int(resp.status.split()[0])
raise cherrypy.HTTPRedirect(resp.message, code)
return resp.message, resp.status, resp.headers | Convert an oic.utils.http_util instance to Flask. | entailment |
def setup_authentication_methods(authn_config, template_env):
"""Add all authentication methods specified in the configuration."""
routing = {}
ac = AuthnBroker()
for authn_method in authn_config:
cls = make_cls_from_name(authn_method["class"])
instance = cls(template_env=template_env, *... | Add all authentication methods specified in the configuration. | entailment |
def setup_endpoints(provider):
"""Setup the OpenID Connect Provider endpoints."""
app_routing = {}
endpoints = [
AuthorizationEndpoint(
pyoidcMiddleware(provider.authorization_endpoint)),
TokenEndpoint(
pyoidcMiddleware(provider.token_endpoint)),
UserinfoEndpo... | Setup the OpenID Connect Provider endpoints. | entailment |
def _webfinger(provider, request, **kwargs):
"""Handle webfinger requests."""
params = urlparse.parse_qs(request)
if params["rel"][0] == OIC_ISSUER:
wf = WebFinger()
return Response(wf.response(params["resource"][0], provider.baseurl),
headers=[("Content-Type", "appli... | Handle webfinger requests. | entailment |
def featuresQuery(self, **kwargs):
"""
Converts a dictionary of keyword arguments into a tuple
of SQL select statements and the list of SQL arguments
"""
# TODO: Optimize by refactoring out string concatenation
sql = ""
sql_rows = "SELECT * FROM FEATURE WHERE id >... | Converts a dictionary of keyword arguments into a tuple
of SQL select statements and the list of SQL arguments | entailment |
def searchFeaturesInDb(
self, startIndex=0, maxResults=None,
referenceName=None, start=None, end=None,
parentId=None, featureTypes=None,
name=None, geneSymbol=None):
"""
Perform a full features query in database.
:param startIndex: int representin... | Perform a full features query in database.
:param startIndex: int representing first record to return
:param maxResults: int representing number of records to return
:param referenceName: string representing reference name, ex 'chr1'
:param start: int position on reference to start sear... | entailment |
def getFeatureById(self, featureId):
"""
Fetch feature by featureID.
:param featureId: the FeatureID as found in GFF3 records
:return: dictionary representing a feature object,
or None if no match is found.
"""
sql = "SELECT * FROM FEATURE WHERE id = ?"
... | Fetch feature by featureID.
:param featureId: the FeatureID as found in GFF3 records
:return: dictionary representing a feature object,
or None if no match is found. | entailment |
def toProtocolElement(self):
"""
Returns the representation of this FeatureSet as the corresponding
ProtocolElement.
"""
gaFeatureSet = protocol.FeatureSet()
gaFeatureSet.id = self.getId()
gaFeatureSet.dataset_id = self.getParentContainer().getId()
gaFeatu... | Returns the representation of this FeatureSet as the corresponding
ProtocolElement. | entailment |
def getCompoundIdForFeatureId(self, featureId):
"""
Returns server-style compound ID for an internal featureId.
:param long featureId: id of feature in database
:return: string representing ID for the specified GA4GH protocol
Feature object in this FeatureSet.
"""
... | Returns server-style compound ID for an internal featureId.
:param long featureId: id of feature in database
:return: string representing ID for the specified GA4GH protocol
Feature object in this FeatureSet. | entailment |
def getFeature(self, compoundId):
"""
Fetches a simulated feature by ID.
:param compoundId: any non-null string
:return: A simulated feature with id set to the same value as the
passed-in compoundId.
":raises: exceptions.ObjectWithIdNotFoundException if None is passe... | Fetches a simulated feature by ID.
:param compoundId: any non-null string
:return: A simulated feature with id set to the same value as the
passed-in compoundId.
":raises: exceptions.ObjectWithIdNotFoundException if None is passed
in for the compoundId. | entailment |
def getFeatures(self, referenceName=None, start=None, end=None,
startIndex=None, maxResults=None,
featureTypes=None, parentId=None,
name=None, geneSymbol=None, numFeatures=10):
"""
Returns a set number of simulated features.
:param ref... | Returns a set number of simulated features.
:param referenceName: name of reference to "search" on
:param start: start coordinate of query
:param end: end coordinate of query
:param startIndex: None or int
:param maxResults: None or int
:param featureTypes: optional list... | entailment |
def populateFromFile(self, dataUrl):
"""
Populates the instance variables of this FeatureSet from the specified
data URL.
"""
self._dbFilePath = dataUrl
self._db = Gff3DbBackend(self._dbFilePath) | Populates the instance variables of this FeatureSet from the specified
data URL. | entailment |
def populateFromRow(self, featureSetRecord):
"""
Populates the instance variables of this FeatureSet from the specified
DB row.
"""
self._dbFilePath = featureSetRecord.dataurl
self.setAttributesJson(featureSetRecord.attributes)
self._db = Gff3DbBackend(self._dbFil... | Populates the instance variables of this FeatureSet from the specified
DB row. | entailment |
def getFeature(self, compoundId):
"""
Returns a protocol.Feature object corresponding to a compoundId
:param compoundId: a datamodel.FeatureCompoundId object
:return: a Feature object.
:raises: exceptions.ObjectWithIdNotFoundException if invalid
compoundId is provided... | Returns a protocol.Feature object corresponding to a compoundId
:param compoundId: a datamodel.FeatureCompoundId object
:return: a Feature object.
:raises: exceptions.ObjectWithIdNotFoundException if invalid
compoundId is provided. | entailment |
def _gaFeatureForFeatureDbRecord(self, feature):
"""
:param feature: The DB Row representing a feature
:return: the corresponding GA4GH protocol.Feature object
"""
gaFeature = protocol.Feature()
gaFeature.id = self.getCompoundIdForFeatureId(feature['id'])
if featu... | :param feature: The DB Row representing a feature
:return: the corresponding GA4GH protocol.Feature object | entailment |
def getFeatures(self, referenceName=None, start=None, end=None,
startIndex=None, maxResults=None,
featureTypes=None, parentId=None,
name=None, geneSymbol=None):
"""
method passed to runSearchRequest to fulfill the request
:param str ref... | method passed to runSearchRequest to fulfill the request
:param str referenceName: name of reference (ex: "chr1")
:param start: castable to int, start position on reference
:param end: castable to int, end position on reference
:param startIndex: none or castable to int
:param ma... | entailment |
def addRnaQuantification(self, rnaQuantification):
"""
Add an rnaQuantification to this rnaQuantificationSet
"""
id_ = rnaQuantification.getId()
self._rnaQuantificationIdMap[id_] = rnaQuantification
self._rnaQuantificationIds.append(id_) | Add an rnaQuantification to this rnaQuantificationSet | entailment |
def toProtocolElement(self):
"""
Converts this rnaQuant into its GA4GH protocol equivalent.
"""
protocolElement = protocol.RnaQuantificationSet()
protocolElement.id = self.getId()
protocolElement.dataset_id = self._parentContainer.getId()
protocolElement.name = se... | Converts this rnaQuant into its GA4GH protocol equivalent. | entailment |
def populateFromFile(self, dataUrl):
"""
Populates the instance variables of this RnaQuantificationSet from the
specified data URL.
"""
self._dbFilePath = dataUrl
self._db = SqliteRnaBackend(self._dbFilePath)
self.addRnaQuants() | Populates the instance variables of this RnaQuantificationSet from the
specified data URL. | entailment |
def populateFromRow(self, quantificationSetRecord):
"""
Populates the instance variables of this RnaQuantificationSet from the
specified DB row.
"""
self._dbFilePath = quantificationSetRecord.dataurl
self.setAttributesJson(quantificationSetRecord.attributes)
self.... | Populates the instance variables of this RnaQuantificationSet from the
specified DB row. | entailment |
def toProtocolElement(self):
"""
Converts this rnaQuant into its GA4GH protocol equivalent.
"""
protocolElement = protocol.RnaQuantification()
protocolElement.id = self.getId()
protocolElement.name = self._name
protocolElement.description = self._description
... | Converts this rnaQuant into its GA4GH protocol equivalent. | entailment |
def addRnaQuantMetadata(self, fields):
"""
data elements are:
Id, annotations, description, name, readGroupId
where annotations is a comma separated list
"""
self._featureSetIds = fields["feature_set_ids"].split(',')
self._description = fields["description"]
... | data elements are:
Id, annotations, description, name, readGroupId
where annotations is a comma separated list | entailment |
def getRnaQuantMetadata(self):
"""
input is tab file with no header. Columns are:
Id, annotations, description, name, readGroupId
where annotation is a comma separated list
"""
rnaQuantId = self.getLocalId()
with self._db as dataSource:
rnaQuantReturn... | input is tab file with no header. Columns are:
Id, annotations, description, name, readGroupId
where annotation is a comma separated list | entailment |
def populateFromFile(self, dataUrl):
"""
Populates the instance variables of this FeatureSet from the specified
data URL.
"""
self._dbFilePath = dataUrl
self._db = SqliteRnaBackend(self._dbFilePath)
self.getRnaQuantMetadata() | Populates the instance variables of this FeatureSet from the specified
data URL. | entailment |
def populateFromRow(self, row):
"""
Populates the instance variables of this FeatureSet from the specified
DB row.
"""
self._dbFilePath = row[b'dataUrl']
self._db = SqliteRnaBackend(self._dbFilePath)
self.getRnaQuantMetadata() | Populates the instance variables of this FeatureSet from the specified
DB row. | entailment |
def getExpressionLevels(
self, threshold=0.0, names=[], startIndex=0, maxResults=0):
"""
Returns the list of ExpressionLevels in this RNA Quantification.
"""
rnaQuantificationId = self.getLocalId()
with self._db as dataSource:
expressionsReturned = dataSou... | Returns the list of ExpressionLevels in this RNA Quantification. | entailment |
def searchRnaQuantificationsInDb(
self, rnaQuantificationId=""):
"""
:param rnaQuantificationId: string restrict search by id
:return an array of dictionaries, representing the returned data.
"""
sql = ("SELECT * FROM RnaQuantification")
sql_args = ()
... | :param rnaQuantificationId: string restrict search by id
:return an array of dictionaries, representing the returned data. | entailment |
def getRnaQuantificationById(self, rnaQuantificationId):
"""
:param rnaQuantificationId: the RNA Quantification ID
:return: dictionary representing an RnaQuantification object,
or None if no match is found.
"""
sql = ("SELECT * FROM RnaQuantification WHERE id = ?")
... | :param rnaQuantificationId: the RNA Quantification ID
:return: dictionary representing an RnaQuantification object,
or None if no match is found. | entailment |
def searchExpressionLevelsInDb(
self, rnaQuantId, names=[], threshold=0.0, startIndex=0,
maxResults=0):
"""
:param rnaQuantId: string restrict search by quantification id
:param threshold: float minimum expression values to return
:return an array of dictionaries,... | :param rnaQuantId: string restrict search by quantification id
:param threshold: float minimum expression values to return
:return an array of dictionaries, representing the returned data. | entailment |
def getExpressionLevelById(self, expressionId):
"""
:param expressionId: the ExpressionLevel ID
:return: dictionary representing an ExpressionLevel object,
or None if no match is found.
"""
sql = ("SELECT * FROM Expression WHERE id = ?")
query = self._dbconn.e... | :param expressionId: the ExpressionLevel ID
:return: dictionary representing an ExpressionLevel object,
or None if no match is found. | entailment |
def populateFromRow(self, callSetRecord):
"""
Populates this CallSet from the specified DB row.
"""
self._biosampleId = callSetRecord.biosampleid
self.setAttributesJson(callSetRecord.attributes) | Populates this CallSet from the specified DB row. | entailment |
def toProtocolElement(self):
"""
Returns the representation of this CallSet as the corresponding
ProtocolElement.
"""
variantSet = self.getParentContainer()
gaCallSet = protocol.CallSet(
biosample_id=self.getBiosampleId())
if variantSet.getCreationTime... | Returns the representation of this CallSet as the corresponding
ProtocolElement. | entailment |
def addVariantAnnotationSet(self, variantAnnotationSet):
"""
Adds the specified variantAnnotationSet to this dataset.
"""
id_ = variantAnnotationSet.getId()
self._variantAnnotationSetIdMap[id_] = variantAnnotationSet
self._variantAnnotationSetIds.append(id_) | Adds the specified variantAnnotationSet to this dataset. | entailment |
def getVariantAnnotationSet(self, id_):
"""
Returns the AnnotationSet in this dataset with the specified 'id'
"""
if id_ not in self._variantAnnotationSetIdMap:
raise exceptions.AnnotationSetNotFoundException(id_)
return self._variantAnnotationSetIdMap[id_] | Returns the AnnotationSet in this dataset with the specified 'id' | entailment |
def addCallSet(self, callSet):
"""
Adds the specfied CallSet to this VariantSet.
"""
callSetId = callSet.getId()
self._callSetIdMap[callSetId] = callSet
self._callSetNameMap[callSet.getLocalId()] = callSet
self._callSetIds.append(callSetId)
self._callSetId... | Adds the specfied CallSet to this VariantSet. | entailment |
def addCallSetFromName(self, sampleName):
"""
Adds a CallSet for the specified sample name.
"""
callSet = CallSet(self, sampleName)
self.addCallSet(callSet) | Adds a CallSet for the specified sample name. | entailment |
def getCallSetByName(self, name):
"""
Returns a CallSet with the specified name, or raises a
CallSetNameNotFoundException if it does not exist.
"""
if name not in self._callSetNameMap:
raise exceptions.CallSetNameNotFoundException(name)
return self._callSetNam... | Returns a CallSet with the specified name, or raises a
CallSetNameNotFoundException if it does not exist. | entailment |
def getCallSet(self, id_):
"""
Returns a CallSet with the specified id, or raises a
CallSetNotFoundException if it does not exist.
"""
if id_ not in self._callSetIdMap:
raise exceptions.CallSetNotFoundException(id_)
return self._callSetIdMap[id_] | Returns a CallSet with the specified id, or raises a
CallSetNotFoundException if it does not exist. | entailment |
def toProtocolElement(self):
"""
Converts this VariantSet into its GA4GH protocol equivalent.
"""
protocolElement = protocol.VariantSet()
protocolElement.id = self.getId()
protocolElement.dataset_id = self.getParentContainer().getId()
protocolElement.reference_set... | Converts this VariantSet into its GA4GH protocol equivalent. | entailment |
def _createGaVariant(self):
"""
Convenience method to set the common fields in a GA Variant
object from this variant set.
"""
ret = protocol.Variant()
if self._creationTime:
ret.created = self._creationTime
if self._updatedTime:
ret.updated... | Convenience method to set the common fields in a GA Variant
object from this variant set. | entailment |
def getVariantId(self, gaVariant):
"""
Returns an ID string suitable for the specified GA Variant
object in this variant set.
"""
md5 = self.hashVariant(gaVariant)
compoundId = datamodel.VariantCompoundId(
self.getCompoundId(), gaVariant.reference_name,
... | Returns an ID string suitable for the specified GA Variant
object in this variant set. | entailment |
def getCallSetId(self, sampleName):
"""
Returns the callSetId for the specified sampleName in this
VariantSet.
"""
compoundId = datamodel.CallSetCompoundId(
self.getCompoundId(), sampleName)
return str(compoundId) | Returns the callSetId for the specified sampleName in this
VariantSet. | entailment |
def hashVariant(cls, gaVariant):
"""
Produces an MD5 hash of the ga variant object to distinguish
it from other variants at the same genomic coordinate.
"""
hash_str = gaVariant.reference_bases + \
str(tuple(gaVariant.alternate_bases))
return hashlib.md5(hash_... | Produces an MD5 hash of the ga variant object to distinguish
it from other variants at the same genomic coordinate. | entailment |
def generateVariant(self, referenceName, position, randomNumberGenerator):
"""
Generate a random variant for the specified position using the
specified random number generator. This generator should be seeded
with a value that is unique to this position so that the same variant
w... | Generate a random variant for the specified position using the
specified random number generator. This generator should be seeded
with a value that is unique to this position so that the same variant
will always be produced regardless of the order it is generated in. | entailment |
def populateFromRow(self, variantSetRecord):
"""
Populates this VariantSet from the specified DB row.
"""
self._created = variantSetRecord.created
self._updated = variantSetRecord.updated
self.setAttributesJson(variantSetRecord.attributes)
self._chromFileMap = {}
... | Populates this VariantSet from the specified DB row. | entailment |
def populateFromFile(self, dataUrls, indexFiles):
"""
Populates this variant set using the specified lists of data
files and indexes. These must be in the same order, such that
the jth index file corresponds to the jth data file.
"""
assert len(dataUrls) == len(indexFiles... | Populates this variant set using the specified lists of data
files and indexes. These must be in the same order, such that
the jth index file corresponds to the jth data file. | entailment |
def populateFromDirectory(self, vcfDirectory):
"""
Populates this VariantSet by examing all the VCF files in the
specified directory. This is mainly used for as a convenience
for testing purposes.
"""
pattern = os.path.join(vcfDirectory, "*.vcf.gz")
dataFiles = []... | Populates this VariantSet by examing all the VCF files in the
specified directory. This is mainly used for as a convenience
for testing purposes. | entailment |
def checkConsistency(self):
"""
Perform consistency check on the variant set
"""
for referenceName, (dataUrl, indexFile) in self._chromFileMap.items():
varFile = pysam.VariantFile(dataUrl, index_filename=indexFile)
try:
for chrom in varFile.index:
... | Perform consistency check on the variant set | entailment |
def _populateFromVariantFile(self, varFile, dataUrl, indexFile):
"""
Populates the instance variables of this VariantSet from the specified
pysam VariantFile object.
"""
if varFile.index is None:
raise exceptions.NotIndexedException(dataUrl)
for chrom in varFi... | Populates the instance variables of this VariantSet from the specified
pysam VariantFile object. | entailment |
def _updateVariantAnnotationSets(self, variantFile, dataUrl):
"""
Updates the variant annotation set associated with this variant using
information in the specified pysam variantFile.
"""
# TODO check the consistency of this between VCF files.
if not self.isAnnotated():
... | Updates the variant annotation set associated with this variant using
information in the specified pysam variantFile. | entailment |
def _updateMetadata(self, variantFile):
"""
Updates the metadata for his variant set based on the specified
variant file
"""
metadata = self._getMetadataFromVcf(variantFile)
if self._metadata is None:
self._metadata = metadata | Updates the metadata for his variant set based on the specified
variant file | entailment |
def _checkMetadata(self, variantFile):
"""
Checks that metadata is consistent
"""
metadata = self._getMetadataFromVcf(variantFile)
if self._metadata is not None and self._metadata != metadata:
raise exceptions.InconsistentMetaDataException(
variantFile... | Checks that metadata is consistent | entailment |
def _checkCallSetIds(self, variantFile):
"""
Checks callSetIds for consistency
"""
if len(self._callSetIdMap) > 0:
callSetIds = set([
self.getCallSetId(sample)
for sample in variantFile.header.samples])
if callSetIds != set(self._ca... | Checks callSetIds for consistency | entailment |
def _updateCallSetIds(self, variantFile):
"""
Updates the call set IDs based on the specified variant file.
"""
if len(self._callSetIdMap) == 0:
for sample in variantFile.header.samples:
self.addCallSetFromName(sample) | Updates the call set IDs based on the specified variant file. | entailment |
def convertVariant(self, record, callSetIds):
"""
Converts the specified pysam variant record into a GA4GH Variant
object. Only calls for the specified list of callSetIds will
be included.
"""
variant = self._createGaVariant()
variant.reference_name = record.conti... | Converts the specified pysam variant record into a GA4GH Variant
object. Only calls for the specified list of callSetIds will
be included. | entailment |
def getPysamVariants(self, referenceName, startPosition, endPosition):
"""
Returns an iterator over the pysam VCF records corresponding to the
specified query.
"""
if referenceName in self._chromFileMap:
varFileName = self._chromFileMap[referenceName]
refe... | Returns an iterator over the pysam VCF records corresponding to the
specified query. | entailment |
def getVariants(self, referenceName, startPosition, endPosition,
callSetIds=[]):
"""
Returns an iterator over the specified variants. The parameters
correspond to the attributes of a GASearchVariantsRequest object.
"""
if callSetIds is None:
callSe... | Returns an iterator over the specified variants. The parameters
correspond to the attributes of a GASearchVariantsRequest object. | entailment |
def getMetadataId(self, metadata):
"""
Returns the id of a metadata
"""
return str(datamodel.VariantSetMetadataCompoundId(
self.getCompoundId(), 'metadata:' + metadata.key)) | Returns the id of a metadata | entailment |
def _createGaVariantAnnotation(self):
"""
Convenience method to set the common fields in a GA VariantAnnotation
object from this variant set.
"""
ret = protocol.VariantAnnotation()
ret.created = self._creationTime
ret.variant_annotation_set_id = self.getId()
... | Convenience method to set the common fields in a GA VariantAnnotation
object from this variant set. | entailment |
def toProtocolElement(self):
"""
Converts this VariantAnnotationSet into its GA4GH protocol equivalent.
"""
protocolElement = protocol.VariantAnnotationSet()
protocolElement.id = self.getId()
protocolElement.variant_set_id = self._variantSet.getId()
protocolElemen... | Converts this VariantAnnotationSet into its GA4GH protocol equivalent. | entailment |
def hashVariantAnnotation(cls, gaVariant, gaVariantAnnotation):
"""
Produces an MD5 hash of the gaVariant and gaVariantAnnotation objects
"""
treffs = [treff.id for treff in gaVariantAnnotation.transcript_effects]
return hashlib.md5(
"{}\t{}\t{}\t".format(
... | Produces an MD5 hash of the gaVariant and gaVariantAnnotation objects | entailment |
def getVariantAnnotationId(self, gaVariant, gaAnnotation):
"""
Produces a stringified compoundId representing a variant
annotation.
:param gaVariant: protocol.Variant
:param gaAnnotation: protocol.VariantAnnotation
:return: compoundId String
"""
md5 = s... | Produces a stringified compoundId representing a variant
annotation.
:param gaVariant: protocol.Variant
:param gaAnnotation: protocol.VariantAnnotation
:return: compoundId String | entailment |
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