INSTRUCTION stringlengths 1 8.43k | RESPONSE stringlengths 75 104k |
|---|---|
Runs the specified function that updates the repo with the specified arguments. This method ensures that all updates are transactional so that if any part of the update fails no changes are made to the repo. | def _updateRepo(self, func, *args, **kwargs):
"""
Runs the specified function that updates the repo with the specified
arguments. This method ensures that all updates are transactional,
so that if any part of the update fails no changes are made to the
repo.
"""
#... |
Adds a new Ontology to this repo. | def addOntology(self):
"""
Adds a new Ontology to this repo.
"""
self._openRepo()
name = self._args.name
filePath = self._getFilePath(self._args.filePath,
self._args.relativePath)
if name is None:
name = getNameFrom... |
Adds a new dataset into this repo. | def addDataset(self):
"""
Adds a new dataset into this repo.
"""
self._openRepo()
dataset = datasets.Dataset(self._args.datasetName)
dataset.setDescription(self._args.description)
dataset.setAttributes(json.loads(self._args.attributes))
self._updateRepo(se... |
Adds a new reference set into this repo. | def addReferenceSet(self):
"""
Adds a new reference set into this repo.
"""
self._openRepo()
name = self._args.name
filePath = self._getFilePath(self._args.filePath,
self._args.relativePath)
if name is None:
name = ... |
Adds a new ReadGroupSet into this repo. | def addReadGroupSet(self):
"""
Adds a new ReadGroupSet into this repo.
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
dataUrl = self._args.dataFile
indexFile = self._args.indexFile
parsed = urlparse.urlparse(dataUrl)
... |
Adds a new VariantSet into this repo. | def addVariantSet(self):
"""
Adds a new VariantSet into this repo.
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
dataUrls = self._args.dataFiles
name = self._args.name
if len(dataUrls) == 1:
if self._args.na... |
Adds a new phenotype association set to this repo. | def addPhenotypeAssociationSet(self):
"""
Adds a new phenotype association set to this repo.
"""
self._openRepo()
name = self._args.name
if name is None:
name = getNameFromPath(self._args.dirPath)
dataset = self._repo.getDatasetByName(self._args.datase... |
Removes a phenotype association set from the repo | def removePhenotypeAssociationSet(self):
"""
Removes a phenotype association set from the repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSetByName(
self._args.nam... |
Removes a referenceSet from the repo. | def removeReferenceSet(self):
"""
Removes a referenceSet from the repo.
"""
self._openRepo()
referenceSet = self._repo.getReferenceSetByName(
self._args.referenceSetName)
def func():
self._updateRepo(self._repo.removeReferenceSet, referenceSet)
... |
Removes a readGroupSet from the repo. | def removeReadGroupSet(self):
"""
Removes a readGroupSet from the repo.
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
readGroupSet = dataset.getReadGroupSetByName(
self._args.readGroupSetName)
def func():
... |
Removes a variantSet from the repo. | def removeVariantSet(self):
"""
Removes a variantSet from the repo.
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
variantSet = dataset.getVariantSetByName(self._args.variantSetName)
def func():
self._updateRepo(sel... |
Removes a dataset from the repo. | def removeDataset(self):
"""
Removes a dataset from the repo.
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
def func():
self._updateRepo(self._repo.removeDataset, dataset)
self._confirmDelete("Dataset", dataset.get... |
Adds a new feature set into this repo | def addFeatureSet(self):
"""
Adds a new feature set into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
filePath = self._getFilePath(self._args.filePath,
self._args.relativePath)
na... |
Removes a feature set from this repo | def removeFeatureSet(self):
"""
Removes a feature set from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
featureSet = dataset.getFeatureSetByName(self._args.featureSetName)
def func():
self._updateRepo(se... |
Adds a new continuous set into this repo | def addContinuousSet(self):
"""
Adds a new continuous set into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
filePath = self._getFilePath(self._args.filePath,
self._args.relativePath)
... |
Removes a continuous set from this repo | def removeContinuousSet(self):
"""
Removes a continuous set from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
continuousSet = dataset.getContinuousSetByName(
self._args.continuousSetName)
... |
Adds a new biosample into this repo | def addBiosample(self):
"""
Adds a new biosample into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
biosample = bio_metadata.Biosample(
dataset, self._args.biosampleName)
biosample.populateFromJson(self._a... |
Removes a biosample from this repo | def removeBiosample(self):
"""
Removes a biosample from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
biosample = dataset.getBiosampleByName(self._args.biosampleName)
def func():
self._updateRepo(self._re... |
Adds a new individual into this repo | def addIndividual(self):
"""
Adds a new individual into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
individual = bio_metadata.Individual(
dataset, self._args.individualName)
individual.populateFromJson(s... |
Removes an individual from this repo | def removeIndividual(self):
"""
Removes an individual from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
individual = dataset.getIndividualByName(self._args.individualName)
def func():
self._updateRepo(se... |
Adds a new peer into this repo | def addPeer(self):
"""
Adds a new peer into this repo
"""
self._openRepo()
try:
peer = peers.Peer(
self._args.url, json.loads(self._args.attributes))
except exceptions.BadUrlException:
raise exceptions.RepoManagerException("The URL ... |
Removes a peer by URL from this repo | def removePeer(self):
"""
Removes a peer by URL from this repo
"""
self._openRepo()
def func():
self._updateRepo(self._repo.removePeer, self._args.url)
self._confirmDelete("Peer", self._args.url, func) |
Removes an ontology from the repo. | def removeOntology(self):
"""
Removes an ontology from the repo.
"""
self._openRepo()
ontology = self._repo.getOntologyByName(self._args.ontologyName)
def func():
self._updateRepo(self._repo.removeOntology, ontology)
self._confirmDelete("Ontology", on... |
Adds an rnaQuantification into this repo | def addRnaQuantification(self):
"""
Adds an rnaQuantification into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
biosampleId = ""
if self._args.biosampleName:
biosample = dataset.getBiosampleByName(self._a... |
Initialize an empty RNA quantification set | def initRnaQuantificationSet(self):
"""
Initialize an empty RNA quantification set
"""
store = rnaseq2ga.RnaSqliteStore(self._args.filePath)
store.createTables() |
Adds an rnaQuantificationSet into this repo | def addRnaQuantificationSet(self):
"""
Adds an rnaQuantificationSet into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
if self._args.name is None:
name = getNameFromPath(self._args.filePath)
else:
... |
Removes an rnaQuantificationSet from this repo | def removeRnaQuantificationSet(self):
"""
Removes an rnaQuantificationSet from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
rnaQuantSet = dataset.getRnaQuantificationSetByName(
self._args.rnaQuantificationSetName... |
Reads RNA Quantification data in one of several formats and stores the data in a sqlite database for use by the GA4GH reference server. | def rnaseq2ga(quantificationFilename, sqlFilename, localName, rnaType,
dataset=None, featureType="gene",
description="", programs="", featureSetNames="",
readGroupSetNames="", biosampleId=""):
"""
Reads RNA Quantification data in one of several formats and stores the da... |
Adds an RNAQuantification to the db. Datafields is a tuple in the order: id feature_set_ids description name read_group_ids programs biosample_id | def addRNAQuantification(self, datafields):
"""
Adds an RNAQuantification to the db. Datafields is a tuple in the
order:
id, feature_set_ids, description, name,
read_group_ids, programs, biosample_id
"""
self._rnaValueList.append(datafields)
if len(self._... |
Adds an Expression to the db. Datafields is a tuple in the order: id rna_quantification_id name expression is_normalized raw_read_count score units conf_low conf_hi | def addExpression(self, datafields):
"""
Adds an Expression to the db. Datafields is a tuple in the order:
id, rna_quantification_id, name, expression,
is_normalized, raw_read_count, score, units, conf_low, conf_hi
"""
self._expressionValueList.append(datafields)
... |
Index columns that are queried. The expression index can take a long time. | def createIndices(self):
"""
Index columns that are queried. The expression index can
take a long time.
"""
sql = '''CREATE INDEX name_index
ON Expression (name)'''
self._cursor.execute(sql)
self._dbConn.commit()
sql = '''CREATE INDEX ex... |
Reads the quantification results file and adds entries to the specified database. | def writeExpression(self, rnaQuantificationId, quantfilename):
"""
Reads the quantification results file and adds entries to the
specified database.
"""
isNormalized = self._isNormalized
units = self._units
with open(quantfilename, "r") as quantFile:
q... |
Fetch sequences from NCBI using the eself interface. | def _fetchSequence(ac, startIndex=None, endIndex=None):
"""Fetch sequences from NCBI using the eself interface.
An interbase interval may be optionally provided with startIndex and
endIndex. NCBI eself will return just the requested subsequence, which
might greatly reduce payload sizes (especially with... |
Creates a new bam header based on the specified header from the parent BAM file. | def createBamHeader(self, baseHeader):
"""
Creates a new bam header based on the specified header from the
parent BAM file.
"""
header = dict(baseHeader)
newSequences = []
for index, referenceInfo in enumerate(header['SQ']):
if index < self.numChromoso... |
Creates the repository for all the data we ve just downloaded. | def createRepo(self):
"""
Creates the repository for all the data we've just downloaded.
"""
repo = datarepo.SqlDataRepository(self.repoPath)
repo.open("w")
repo.initialise()
referenceSet = references.HtslibReferenceSet("GRCh37-subset")
referenceSet.popul... |
A helper function used just to help modularize the code a bit. | def _configure_backend(app):
"""A helper function used just to help modularize the code a bit."""
# Allocate the backend
# We use URLs to specify the backend. Currently we have file:// URLs (or
# URLs with no scheme) for the SqlDataRepository, and special empty:// and
# simulated:// URLs for empty o... |
TODO Document this critical function! What does it do? What does it assume? | def configure(configFile=None, baseConfig="ProductionConfig",
port=8000, extraConfig={}):
"""
TODO Document this critical function! What does it do? What does
it assume?
"""
file_handler = StreamHandler()
file_handler.setLevel(logging.WARNING)
app.logger.addHandler(file_handler... |
Returns a Flask response object for the specified data and HTTP status. | def getFlaskResponse(responseString, httpStatus=200):
"""
Returns a Flask response object for the specified data and HTTP status.
"""
return flask.Response(responseString, status=httpStatus, mimetype=MIMETYPE) |
Handles the specified HTTP POST request which maps to the specified protocol handler endpoint and protocol request class. | def handleHttpPost(request, endpoint):
"""
Handles the specified HTTP POST request, which maps to the specified
protocol handler endpoint and protocol request class.
"""
if request.mimetype and request.mimetype != MIMETYPE:
raise exceptions.UnsupportedMediaTypeException()
request = reque... |
Handles an exception that occurs somewhere in the process of handling a request. | def handleException(exception):
"""
Handles an exception that occurs somewhere in the process of handling
a request.
"""
serverException = exception
if not isinstance(exception, exceptions.BaseServerException):
with app.test_request_context():
app.log_exception(exception)
... |
If we are not logged in this generates the redirect URL to the OIDC provider and returns the redirect response: return: A redirect response to the OIDC provider | def startLogin():
"""
If we are not logged in, this generates the redirect URL to the OIDC
provider and returns the redirect response
:return: A redirect response to the OIDC provider
"""
flask.session["state"] = oic.oauth2.rndstr(SECRET_KEY_LENGTH)
flask.session["nonce"] = oic.oauth2.rndstr... |
The request will have a parameter key if it came from the command line client or have a session key of key if it s the browser. If the token is not found start the login process. | def checkAuthentication():
"""
The request will have a parameter 'key' if it came from the command line
client, or have a session key of 'key' if it's the browser.
If the token is not found, start the login process.
If there is no oidcClient, we are running naked and we don't check.
If we're be... |
Handles the specified flask request for one of the GET URLs Invokes the specified endpoint to generate a response. | def handleFlaskGetRequest(id_, flaskRequest, endpoint):
"""
Handles the specified flask request for one of the GET URLs
Invokes the specified endpoint to generate a response.
"""
if flaskRequest.method == "GET":
return handleHttpGet(id_, endpoint)
else:
raise exceptions.MethodNot... |
Handles the specified flask request for one of the POST URLS Invokes the specified endpoint to generate a response. | def handleFlaskPostRequest(flaskRequest, endpoint):
"""
Handles the specified flask request for one of the POST URLS
Invokes the specified endpoint to generate a response.
"""
if flaskRequest.method == "POST":
return handleHttpPost(flaskRequest, endpoint)
elif flaskRequest.method == "OPT... |
Returns the list of ReferenceSets for this server. | def getVariantAnnotationSets(self, datasetId):
"""
Returns the list of ReferenceSets for this server.
"""
# TODO this should be displayed per-variant set, not per dataset.
variantAnnotationSets = []
dataset = app.backend.getDataRepository().getDataset(datasetId)
f... |
This decorator wraps a view function so that it is protected when Auth0 is enabled. This means that any request will be expected to have a signed token in the authorization header if the AUTH0_ENABLED configuration setting is True. | def auth_decorator(app=None):
"""
This decorator wraps a view function so that it is protected when Auth0
is enabled. This means that any request will be expected to have a signed
token in the authorization header if the `AUTH0_ENABLED` configuration
setting is True.
The authorization header wi... |
A function that threads the header through decoding and returns a tuple of the token and payload if successful. This does not fully authenticate a request.: param auth_header:: param client_id:: param client_secret:: return: ( token profile ) | def decode_header(auth_header, client_id, client_secret):
"""
A function that threads the header through decoding and returns a tuple
of the token and payload if successful. This does not fully authenticate
a request.
:param auth_header:
:param client_id:
:param client_secret:
:return: (... |
Logs out the current session by removing it from the cache. This is expected to only occur when a session has | def logout(cache):
"""
Logs out the current session by removing it from the cache. This is
expected to only occur when a session has
"""
cache.set(flask.session['auth0_key'], None)
flask.session.clear()
return True |
This function will generate a view function that can be used to handle the return from Auth0. The callback is a redirected session from auth0 that includes the token we can use to authenticate that session. | def callback_maker(
cache=None, domain='', client_id='',
client_secret='', redirect_uri=''):
"""
This function will generate a view function that can be used to handle
the return from Auth0. The "callback" is a redirected session from auth0
that includes the token we can use to authentic... |
This function will generate a view function that can be used to handle the return from Auth0. The callback is a redirected session from auth0 that includes the token we can use to authenticate that session. | def render_login(
app=None, scopes='', redirect_uri='', domain='', client_id=''):
"""
This function will generate a view function that can be used to handle
the return from Auth0. The "callback" is a redirected session from auth0
that includes the token we can use to authenticate that session.
... |
Renders a view from the app and a key that lets the current session grab its token.: param app:: param key:: return: Rendered view | def render_key(app, key=""):
"""
Renders a view from the app and a key that lets the current session grab
its token.
:param app:
:param key:
:return: Rendered view
"""
return app.jinja_env.from_string(KEY_HTML).render(
key=key) |
Takes the header and tries to return an active token and decoded payload.: param auth_header:: param client_id:: param client_secret:: return: ( token profile ) | def _decode_header(auth_header, client_id, client_secret):
"""
Takes the header and tries to return an active token and decoded
payload.
:param auth_header:
:param client_id:
:param client_secret:
:return: (token, profile)
"""
try:
token = auth_header.split()[1]
paylo... |
Accepts the cache and ID token and checks to see if the profile is currently logged in. If so return the token otherwise throw a NotAuthenticatedException.: param cache:: param token:: return: | def is_active(cache, token):
"""
Accepts the cache and ID token and checks to see if the profile is
currently logged in. If so, return the token, otherwise throw a
NotAuthenticatedException.
:param cache:
:param token:
:return:
"""
profile = cache.get(token)
if not profile:
... |
Adds the specified reference to this ReferenceSet. | def addReference(self, reference):
"""
Adds the specified reference to this ReferenceSet.
"""
id_ = reference.getId()
self._referenceIdMap[id_] = reference
self._referenceNameMap[reference.getLocalId()] = reference
self._referenceIds.append(id_) |
Sets the species an OntologyTerm to the specified value given as a JSON string. | def setSpeciesFromJson(self, speciesJson):
"""
Sets the species, an OntologyTerm, to the specified value, given as
a JSON string.
See the documentation for details of this field.
"""
try:
parsed = protocol.fromJson(speciesJson, protocol.OntologyTerm)
... |
Returns the reference with the specified name. | def getReferenceByName(self, name):
"""
Returns the reference with the specified name.
"""
if name not in self._referenceNameMap:
raise exceptions.ReferenceNameNotFoundException(name)
return self._referenceNameMap[name] |
Returns the Reference with the specified ID or raises a ReferenceNotFoundException if it does not exist. | def getReference(self, id_):
"""
Returns the Reference with the specified ID or raises a
ReferenceNotFoundException if it does not exist.
"""
if id_ not in self._referenceIdMap:
raise exceptions.ReferenceNotFoundException(id_)
return self._referenceIdMap[id_] |
Returns the MD5 checksum for this reference set. This checksum is calculated by making a list of Reference. md5checksum for all Reference s in this set. We then sort this list and take the MD5 hash of all the strings concatenated together. | def getMd5Checksum(self):
"""
Returns the MD5 checksum for this reference set. This checksum is
calculated by making a list of `Reference.md5checksum` for all
`Reference`s in this set. We then sort this list, and take the
MD5 hash of all the strings concatenated together.
... |
Returns the GA4GH protocol representation of this ReferenceSet. | def toProtocolElement(self):
"""
Returns the GA4GH protocol representation of this ReferenceSet.
"""
ret = protocol.ReferenceSet()
ret.assembly_id = pb.string(self.getAssemblyId())
ret.description = pb.string(self.getDescription())
ret.id = self.getId()
re... |
Returns the GA4GH protocol representation of this Reference. | def toProtocolElement(self):
"""
Returns the GA4GH protocol representation of this Reference.
"""
reference = protocol.Reference()
reference.id = self.getId()
reference.is_derived = self.getIsDerived()
reference.length = self.getLength()
reference.md5check... |
Checks to ensure that the query range is valid within this reference. If not raise ReferenceRangeErrorException. | def checkQueryRange(self, start, end):
"""
Checks to ensure that the query range is valid within this reference.
If not, raise ReferenceRangeErrorException.
"""
condition = (
(start < 0 or end > self.getLength()) or
start > end or start == end)
if ... |
Populates the instance variables of this ReferencSet from the data URL. | def populateFromFile(self, dataUrl):
"""
Populates the instance variables of this ReferencSet from the
data URL.
"""
self._dataUrl = dataUrl
fastaFile = self.getFastaFile()
for referenceName in fastaFile.references:
reference = HtslibReference(self, re... |
Populates this reference set from the values in the specified DB row. | def populateFromRow(self, referenceSetRecord):
"""
Populates this reference set from the values in the specified DB
row.
"""
self._dataUrl = referenceSetRecord.dataurl
self._description = referenceSetRecord.description
self._assemblyId = referenceSetRecord.assembl... |
Populates this reference from the values in the specified DB row. | def populateFromRow(self, referenceRecord):
"""
Populates this reference from the values in the specified DB row.
"""
self._length = referenceRecord.length
self._isDerived = bool(referenceRecord.isderived)
self._md5checksum = referenceRecord.md5checksum
species = ... |
Given a set of results from our search query return the details ( feature environment phenotype ) | def _extractAssociationsDetails(self, associations):
"""
Given a set of results from our search query, return the
`details` (feature,environment,phenotype)
"""
detailedURIRef = []
for row in associations.bindings:
if 'feature' in row:
detailedU... |
Given a list of uriRefs return a list of dicts: { subject: s predicate: p object: o } all values are strings | def _detailTuples(self, uriRefs):
"""
Given a list of uriRefs, return a list of dicts:
{'subject': s, 'predicate': p, 'object': o }
all values are strings
"""
details = []
for uriRef in uriRefs:
for subject, predicate, object_ in self._rdfGraph.triples... |
Given a binding from the sparql query result create a dict of plain text | def _bindingsToDict(self, bindings):
"""
Given a binding from the sparql query result,
create a dict of plain text
"""
myDict = {}
for key, val in bindings.iteritems():
myDict[key.toPython().replace('?', '')] = val.toPython()
return myDict |
Given a filename add it to the graph | def _addDataFile(self, filename):
"""
Given a filename, add it to the graph
"""
if filename.endswith('.ttl'):
self._rdfGraph.parse(filename, format='n3')
else:
self._rdfGraph.parse(filename, format='xml') |
Given a uriRef return a dict of all the details for that Ref use the uriRef as the id of the dict | def _getDetails(self, uriRef, associations_details):
"""
Given a uriRef, return a dict of all the details for that Ref
use the uriRef as the 'id' of the dict
"""
associationDetail = {}
for detail in associations_details:
if detail['subject'] == uriRef:
... |
Formats several external identifiers for query | def _formatExternalIdentifiers(self, element, element_type):
"""
Formats several external identifiers for query
"""
elementClause = None
elements = []
if not issubclass(element.__class__, dict):
element = protocol.toJsonDict(element)
if element['extern... |
Formats a single external identifier for query | def _formatExternalIdentifier(self, element, element_type):
"""
Formats a single external identifier for query
"""
if "http" not in element['database']:
term = "{}:{}".format(element['database'], element['identifier'])
namespaceTerm = self._toNamespaceURL(term)
... |
Formats the ontology terms for query | def _formatOntologyTerm(self, element, element_type):
"""
Formats the ontology terms for query
"""
elementClause = None
if isinstance(element, dict) and element.get('terms'):
elements = []
for _term in element['terms']:
if _term.get('id'):
... |
Formats the ontology term object for query | def _formatOntologyTermObject(self, terms, element_type):
"""
Formats the ontology term object for query
"""
elementClause = None
if not isinstance(terms, collections.Iterable):
terms = [terms]
elements = []
for term in terms:
if term.term_... |
Formats a set of identifiers for query | def _formatIds(self, element, element_type):
"""
Formats a set of identifiers for query
"""
elementClause = None
if isinstance(element, collections.Iterable):
elements = []
for _id in element:
elements.append('?{} = <{}> '.format(
... |
Formats elements passed into parts of a query for filtering | def _formatEvidence(self, elements):
"""
Formats elements passed into parts of a query for filtering
"""
elementClause = None
filters = []
for evidence in elements:
if evidence.description:
elementClause = 'regex(?{}, "{}")'.format(
... |
Given a url identifier return identifier portion Leverages prefixes already in graph namespace Returns None if no match Ex. http:// www. drugbank. ca/ drugs/ DB01268 - > DB01268 | def _getIdentifier(self, url):
"""
Given a url identifier return identifier portion
Leverages prefixes already in graph namespace
Returns None if no match
Ex. "http://www.drugbank.ca/drugs/DB01268" -> "DB01268"
"""
for prefix, namespace in self._rdfGraph.namespac... |
Given a url return namespace prefix. Leverages prefixes already in graph namespace Ex. http:// www. drugbank. ca/ drugs/ DDD - > http:// www. drugbank. ca/ drugs/ | def _getPrefixURL(self, url):
"""
Given a url return namespace prefix.
Leverages prefixes already in graph namespace
Ex. "http://www.drugbank.ca/drugs/DDD"
-> "http://www.drugbank.ca/drugs/"
"""
for prefix, namespace in self._rdfGraph.namespaces():
... |
given an association dict return a protocol. FeaturePhenotypeAssociation | def _toGA4GH(self, association, featureSets=[]):
"""
given an association dict,
return a protocol.FeaturePhenotypeAssociation
"""
# The association dict has the keys: environment, environment
# label, evidence, feature label, phenotype and sources. Each
# key's v... |
This query is the main search mechanism. It queries the graph for annotations that match the AND of [ feature environment phenotype ]. | def getAssociations(
self, request=None, featureSets=[]):
"""
This query is the main search mechanism.
It queries the graph for annotations that match the
AND of [feature,environment,phenotype].
"""
if len(featureSets) == 0:
featureSets = self.getP... |
Generate a formatted sparql query with appropriate filters | def _formatFilterQuery(self, request=None, featureSets=[]):
"""
Generate a formatted sparql query with appropriate filters
"""
query = self._baseQuery()
filters = []
if issubclass(request.__class__,
protocol.SearchGenotypePhenotypeRequest):
... |
Filters request for phenotype search requests | def _filterSearchPhenotypesRequest(self, request):
"""
Filters request for phenotype search requests
"""
filters = []
if request.id:
filters.append("?phenotype = <{}>".format(request.id))
if request.description:
filters.append(
're... |
Parse the line describing the mode. | def parseStep(self, line):
"""
Parse the line describing the mode.
One of:
variableStep chrom=<reference> [span=<window_size>]
fixedStep chrom=<reference> start=<position> step=<step_interval>
[span=<window_size>]
Span is optional, defaulting to 1. It ... |
Read a wiggle line. If it is a data line add values to the protocol object. | def readWiggleLine(self, line):
"""
Read a wiggle line. If it is a data line, add values to the
protocol object.
"""
if(line.isspace() or line.startswith("#")
or line.startswith("browser") or line.startswith("track")):
return
elif line.startswi... |
Return a continuous protocol object satsifiying the given query parameters from the given wiggle file handle. | def wiggleFileHandleToProtocol(self, fileHandle):
"""
Return a continuous protocol object satsifiying the given query
parameters from the given wiggle file handle.
"""
for line in fileHandle:
self.readWiggleLine(line)
return self._data |
Check the reference for security. Tries to avoid any characters necessary for doing a script injection. | def checkReference(self, reference):
"""
Check the reference for security. Tries to avoid any characters
necessary for doing a script injection.
"""
pattern = re.compile(r'[\s,;"\'&\\]')
if pattern.findall(reference.strip()):
return False
return True |
Use pyBigWig package to read a BigWig file for the given range and return a protocol object. | def readValuesPyBigWig(self, reference, start, end):
"""
Use pyBigWig package to read a BigWig file for the
given range and return a protocol object.
pyBigWig returns an array of values that fill the query range.
Not sure if it is possible to get the step and span.
This... |
Read a bigwig file and return a protocol object with values within the query range. | def readValuesBigWigToWig(self, reference, start, end):
"""
Read a bigwig file and return a protocol object with values
within the query range.
This method uses the bigWigToWig command line tool from UCSC
GoldenPath. The tool is used to return values within a query region.
... |
Returns the representation of this ContinuousSet as the corresponding ProtocolElement. | def toProtocolElement(self):
"""
Returns the representation of this ContinuousSet as the corresponding
ProtocolElement.
"""
gaContinuousSet = protocol.ContinuousSet()
gaContinuousSet.id = self.getId()
gaContinuousSet.dataset_id = self.getParentContainer().getId()
... |
Populates the instance variables of this ContinuousSet from the specified DB row. | def populateFromRow(self, continuousSetRecord):
"""
Populates the instance variables of this ContinuousSet from the
specified DB row.
"""
self._filePath = continuousSetRecord.dataurl
self.setAttributesJson(continuousSetRecord.attributes) |
Method passed to runSearchRequest to fulfill the request to yield continuous protocol objects that satisfy the given query. | def getContinuous(self, referenceName=None, start=None, end=None):
"""
Method passed to runSearchRequest to fulfill the request to
yield continuous protocol objects that satisfy the given query.
:param str referenceName: name of reference (ex: "chr1")
:param start: castable to i... |
Returns a set number of simulated continuous data. | def getContinuousData(self, referenceName=None, start=None, end=None):
"""
Returns a set number of simulated continuous data.
:param referenceName: name of reference to "search" on
:param start: start coordinate of query
:param end: end coordinate of query
:return: Yield... |
Will load a templated configuration on the device. | def load_template(self, template_name, template_source=None,
template_path=None, **template_vars):
"""
Will load a templated configuration on the device.
:param cls: Instance of the driver class.
:param template_name: Identifies the template name.
:param te... |
Executes ping on the device and returns a dictionary with the result | def ping(self, destination, source=c.PING_SOURCE, ttl=c.PING_TTL, timeout=c.PING_TIMEOUT,
size=c.PING_SIZE, count=c.PING_COUNT, vrf=c.PING_VRF):
"""
Executes ping on the device and returns a dictionary with the result
:param destination: Host or IP Address of the destination
... |
Only useful for EOS | def run_commands(self, commands):
"""Only useful for EOS"""
if "eos" in self.profile:
return list(self.parent.cli(commands).values())[0]
else:
raise AttributeError("MockedDriver instance has not attribute '_rpc'") |
Applies a TextFSM template over a raw text and return the matching table. | def textfsm_extractor(cls, template_name, raw_text):
"""
Applies a TextFSM template over a raw text and return the matching table.
Main usage of this method will be to extract data form a non-structured output
from a network device and return the values in a table format.
:param cls: Instance of t... |
Extracts the text value from an XML tree using XPath. In case of error will return a default value. | def find_txt(xml_tree, path, default=''):
"""
Extracts the text value from an XML tree, using XPath.
In case of error, will return a default value.
:param xml_tree: the XML Tree object. Assumed is <type 'lxml.etree._Element'>.
:param path: XPath to be applied, in order to extract the desired da... |
Converts data to a specific datatype. In case of error will return a default value. | def convert(to, who, default=u''):
"""
Converts data to a specific datatype.
In case of error, will return a default value.
:param to: datatype to be casted to.
:param who: value to cast.
:param default: value to return in case of error.
:return: a str value.
"""
if who is ... |
Converts a raw string to a standardised MAC Address EUI Format. | def mac(raw):
"""
Converts a raw string to a standardised MAC Address EUI Format.
:param raw: the raw string containing the value of the MAC Address
:return: a string with the MAC Address in EUI format
Example:
.. code-block:: python
>>> mac('0123.4567.89ab')
u'01:23:45:67:89... |
Compare numerical values. You can use <%d > %d. | def compare_numeric(src_num, dst_num):
"""Compare numerical values. You can use '<%d','>%d'."""
dst_num = float(dst_num)
match = numeric_compare_regex.match(src_num)
if not match:
error = "Failed numeric comparison. Collected: {}. Expected: {}".format(dst_num, src_num)
raise ValueError(... |
Converts a string in the format: | def colon_separated_string_to_dict(string, separator=':'):
'''
Converts a string in the format:
Name: Et3
Switchport: Enabled
Administrative Mode: trunk
Operational Mode: trunk
MAC Address Learning: enabled
Access Mode VLAN: 3 (VLAN0003)
Trunking Native M... |
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