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value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
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train | RepoManager._updateRepo | Runs the specified function that updates the repo with the specified
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"""
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
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"""
#... | def _updateRepo(self, func, *args, **kwargs):
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Runs the specified function that updates the repo with the specified
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train | RepoManager.addOntology | Adds a new Ontology to this repo. | ga4gh/server/cli/repomanager.py | def addOntology(self):
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Adds a new Ontology to this repo.
"""
self._openRepo()
name = self._args.name
filePath = self._getFilePath(self._args.filePath,
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name = getNameFrom... | def addOntology(self):
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train | RepoManager.addDataset | Adds a new dataset into this repo. | ga4gh/server/cli/repomanager.py | def addDataset(self):
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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... | def addDataset(self):
"""
Adds a new dataset into this repo.
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self._openRepo()
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dataset.setDescription(self._args.description)
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train | RepoManager.addReferenceSet | Adds a new reference set into this repo. | ga4gh/server/cli/repomanager.py | def addReferenceSet(self):
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Adds a new reference set into this repo.
"""
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name = self._args.name
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train | RepoManager.addReadGroupSet | Adds a new ReadGroupSet into this repo. | ga4gh/server/cli/repomanager.py | def addReadGroupSet(self):
"""
Adds a new ReadGroupSet into this repo.
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
dataUrl = self._args.dataFile
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Adds a new ReadGroupSet into this repo.
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train | RepoManager.addVariantSet | Adds a new VariantSet into this repo. | ga4gh/server/cli/repomanager.py | 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
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Adds a new VariantSet into this repo.
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train | RepoManager.addPhenotypeAssociationSet | Adds a new phenotype association set to this repo. | ga4gh/server/cli/repomanager.py | def addPhenotypeAssociationSet(self):
"""
Adds a new phenotype association set to this repo.
"""
self._openRepo()
name = self._args.name
if name is None:
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dataset = self._repo.getDatasetByName(self._args.datase... | def addPhenotypeAssociationSet(self):
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Adds a new phenotype association set to this repo.
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train | RepoManager.removePhenotypeAssociationSet | Removes a phenotype association set from the repo | ga4gh/server/cli/repomanager.py | def removePhenotypeAssociationSet(self):
"""
Removes a phenotype association set from the repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSetByName(
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Removes a phenotype association set from the repo
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train | RepoManager.removeReferenceSet | Removes a referenceSet from the repo. | ga4gh/server/cli/repomanager.py | def removeReferenceSet(self):
"""
Removes a referenceSet from the repo.
"""
self._openRepo()
referenceSet = self._repo.getReferenceSetByName(
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def func():
self._updateRepo(self._repo.removeReferenceSet, referenceSet)
... | def removeReferenceSet(self):
"""
Removes a referenceSet from the repo.
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train | RepoManager.removeReadGroupSet | Removes a readGroupSet from the repo. | ga4gh/server/cli/repomanager.py | def removeReadGroupSet(self):
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Removes a readGroupSet from the repo.
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self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
readGroupSet = dataset.getReadGroupSetByName(
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Removes a readGroupSet from the repo.
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train | RepoManager.removeVariantSet | Removes a variantSet from the repo. | ga4gh/server/cli/repomanager.py | def removeVariantSet(self):
"""
Removes a variantSet from the repo.
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self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
variantSet = dataset.getVariantSetByName(self._args.variantSetName)
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train | RepoManager.removeDataset | Removes a dataset from the repo. | ga4gh/server/cli/repomanager.py | def removeDataset(self):
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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... | def removeDataset(self):
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Removes a dataset from the repo.
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self._openRepo()
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train | RepoManager.addFeatureSet | Adds a new feature set into this repo | ga4gh/server/cli/repomanager.py | def addFeatureSet(self):
"""
Adds a new feature set into this repo
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self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
filePath = self._getFilePath(self._args.filePath,
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"""
Adds a new feature set into this repo
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self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
filePath = self._getFilePath(self._args.filePath,
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train | RepoManager.removeFeatureSet | Removes a feature set from this repo | ga4gh/server/cli/repomanager.py | 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():
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Removes a feature set from this repo
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train | RepoManager.addContinuousSet | Adds a new continuous set into this repo | ga4gh/server/cli/repomanager.py | 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,
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Adds a new continuous set into this repo
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dataset = self._repo.getDatasetByName(self._args.datasetName)
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train | RepoManager.removeContinuousSet | Removes a continuous set from this repo | ga4gh/server/cli/repomanager.py | def removeContinuousSet(self):
"""
Removes a continuous set from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
continuousSet = dataset.getContinuousSetByName(
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Removes a continuous set from this repo
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train | RepoManager.addBiosample | Adds a new biosample into this repo | ga4gh/server/cli/repomanager.py | def addBiosample(self):
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Adds a new biosample into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
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Adds a new biosample into this repo
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self._openRepo()
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train | RepoManager.removeBiosample | Removes a biosample from this repo | ga4gh/server/cli/repomanager.py | def removeBiosample(self):
"""
Removes a biosample from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
biosample = dataset.getBiosampleByName(self._args.biosampleName)
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Removes a biosample from this repo
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train | RepoManager.addIndividual | Adds a new individual into this repo | ga4gh/server/cli/repomanager.py | def addIndividual(self):
"""
Adds a new individual into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
individual = bio_metadata.Individual(
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individual.populateFromJson(s... | def addIndividual(self):
"""
Adds a new individual into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
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dataset, self._args.individualName)
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train | RepoManager.removeIndividual | Removes an individual from this repo | ga4gh/server/cli/repomanager.py | def removeIndividual(self):
"""
Removes an individual from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
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train | RepoManager.addPeer | Adds a new peer into this repo | ga4gh/server/cli/repomanager.py | def addPeer(self):
"""
Adds a new peer into this repo
"""
self._openRepo()
try:
peer = peers.Peer(
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raise exceptions.RepoManagerException("The URL ... | def addPeer(self):
"""
Adds a new peer into this repo
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train | RepoManager.removePeer | Removes a peer by URL from this repo | ga4gh/server/cli/repomanager.py | 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) | def removePeer(self):
"""
Removes a peer by URL from this repo
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self._openRepo()
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train | RepoManager.removeOntology | Removes an ontology from the repo. | ga4gh/server/cli/repomanager.py | 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... | def removeOntology(self):
"""
Removes an ontology from the repo.
"""
self._openRepo()
ontology = self._repo.getOntologyByName(self._args.ontologyName)
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train | RepoManager.addRnaQuantification | Adds an rnaQuantification into this repo | ga4gh/server/cli/repomanager.py | 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... | def addRnaQuantification(self):
"""
Adds an rnaQuantification into this repo
"""
self._openRepo()
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train | RepoManager.initRnaQuantificationSet | Initialize an empty RNA quantification set | ga4gh/server/cli/repomanager.py | def initRnaQuantificationSet(self):
"""
Initialize an empty RNA quantification set
"""
store = rnaseq2ga.RnaSqliteStore(self._args.filePath)
store.createTables() | def initRnaQuantificationSet(self):
"""
Initialize an empty RNA quantification set
"""
store = rnaseq2ga.RnaSqliteStore(self._args.filePath)
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train | RepoManager.addRnaQuantificationSet | Adds an rnaQuantificationSet into this repo | ga4gh/server/cli/repomanager.py | 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)
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"""
Adds an rnaQuantificationSet into this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
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name = getNameFromPath(self._args.filePath)
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train | RepoManager.removeRnaQuantificationSet | Removes an rnaQuantificationSet from this repo | ga4gh/server/cli/repomanager.py | def removeRnaQuantificationSet(self):
"""
Removes an rnaQuantificationSet from this repo
"""
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
rnaQuantSet = dataset.getRnaQuantificationSetByName(
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Removes an rnaQuantificationSet from this repo
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self._openRepo()
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Supports the following quantification output types:
Cufflinks, kallisto, RSEM. | ga4gh/server/repo/rnaseq2ga.py | def rnaseq2ga(quantificationFilename, sqlFilename, localName, rnaType,
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train | RnaSqliteStore.addRNAQuantification | Adds an RNAQuantification to the db. Datafields is a tuple in the
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id, feature_set_ids, description, name,
read_group_ids, programs, biosample_id | ga4gh/server/repo/rnaseq2ga.py | def addRNAQuantification(self, datafields):
"""
Adds an RNAQuantification to the db. Datafields is a tuple in the
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id, feature_set_ids, description, name,
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self._rnaValueList.append(datafields)
if len(self._... | def addRNAQuantification(self, datafields):
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train | RnaSqliteStore.addExpression | 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 | ga4gh/server/repo/rnaseq2ga.py | 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)
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Adds an Expression to the db. Datafields is a tuple in the order:
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train | RnaSqliteStore.createIndices | Index columns that are queried. The expression index can
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"""
Index columns that are queried. The expression index can
take a long time.
"""
sql = '''CREATE INDEX name_index
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self._cursor.execute(sql)
self._dbConn.commit()
sql = '''CREATE INDEX ex... | def createIndices(self):
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Index columns that are queried. The expression index can
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train | AbstractWriter.writeExpression | Reads the quantification results file and adds entries to the
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"""
Reads the quantification results file and adds entries to the
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"""
isNormalized = self._isNormalized
units = self._units
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train | AbstractFileDownloader.createRepo | Creates the repository for all the data we've just downloaded. | scripts/download_example_data.py | def createRepo(self):
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"""
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repo.open("w")
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TODO Document this critical function! What does it do? What does
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train | getFlaskResponse | Returns a Flask response object for the specified data and HTTP status. | ga4gh/server/frontend.py | def getFlaskResponse(responseString, httpStatus=200):
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Returns a Flask response object for the specified data and HTTP status.
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Handles the specified HTTP POST request, which maps to the specified
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train | handleException | Handles an exception that occurs somewhere in the process of handling
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"""
Handles an exception that occurs somewhere in the process of handling
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"""
serverException = exception
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train | startLogin | If we are not logged in, this generates the redirect URL to the OIDC
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"""
If we are not logged in, this generates the redirect URL to the OIDC
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"""
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"""
Handles the specified flask request for one of the GET URLs
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train | ServerStatus.getVariantAnnotationSets | Returns the list of ReferenceSets for this server. | ga4gh/server/frontend.py | def getVariantAnnotationSets(self, datasetId):
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Returns the list of ReferenceSets for this server.
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variantAnnotationSets = []
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train | decode_header | A function that threads the header through decoding and returns a tuple
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:param auth_header:
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A function that threads the header through decoding and returns a tuple
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:param auth_header:
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:param client_secret:
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train | logout | Logs out the current session by removing it from the cache. This is
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"""
Logs out the current session by removing it from the cache. This is
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"""
cache.set(flask.session['auth0_key'], None)
flask.session.clear()
return True | def logout(cache):
"""
Logs out the current session by removing it from the cache. This is
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"""
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train | callback_maker | This function will generate a view function that can be used to handle
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that includes the token we can use to authenticate that session.
If the session is properly authenticated Auth0 will provide a code so our
application can iden... | ga4gh/server/auth/__init__.py | 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
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train | render_login | This function will generate a view function that can be used to handle
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"""
This function will generate a view function that can be used to handle
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train | render_key | Renders a view from the app and a key that lets the current session grab
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return app.jinja_env.from_string(KEY_HTML).render(
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train | _decode_header | Takes the header and tries to return an active token and decoded
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:param client_id:
:param client_secret:
:return: (token, profile) | ga4gh/server/auth/__init__.py | def _decode_header(auth_header, client_id, client_secret):
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:param auth_header:
:param client_id:
:param client_secret:
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train | is_active | Accepts the cache and ID token and checks to see if the profile is
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:param cache:
:param token:
:return: | ga4gh/server/auth/__init__.py | def is_active(cache, token):
"""
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:param token:
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train | AbstractReferenceSet.addReference | Adds the specified reference to this ReferenceSet. | ga4gh/server/datamodel/references.py | def addReference(self, reference):
"""
Adds the specified reference to this ReferenceSet.
"""
id_ = reference.getId()
self._referenceIdMap[id_] = reference
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train | AbstractReferenceSet.setSpeciesFromJson | Sets the species, an OntologyTerm, to the specified value, given as
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See the documentation for details of this field. | ga4gh/server/datamodel/references.py | def setSpeciesFromJson(self, speciesJson):
"""
Sets the species, an OntologyTerm, to the specified value, given as
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See the documentation for details of this field.
"""
try:
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Sets the species, an OntologyTerm, to the specified value, given as
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train | AbstractReferenceSet.getReferenceByName | Returns the reference with the specified name. | ga4gh/server/datamodel/references.py | 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] | def getReferenceByName(self, name):
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Returns the reference with the specified name.
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train | AbstractReferenceSet.getReference | Returns the Reference with the specified ID or raises a
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"""
Returns the Reference with the specified ID or raises a
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"""
if id_ not in self._referenceIdMap:
raise exceptions.ReferenceNotFoundException(id_)
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train | AbstractReferenceSet.getMd5Checksum | Returns the MD5 checksum for this reference set. This checksum is
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`Reference`s in this set. We then sort this list, and take the
MD5 hash of all the strings concatenated together. | ga4gh/server/datamodel/references.py | def getMd5Checksum(self):
"""
Returns the MD5 checksum for this reference set. This checksum is
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... | def getMd5Checksum(self):
"""
Returns the MD5 checksum for this reference set. This checksum is
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`Reference`s in this set. We then sort this list, and take the
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train | AbstractReferenceSet.toProtocolElement | Returns the GA4GH protocol representation of this ReferenceSet. | ga4gh/server/datamodel/references.py | 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()
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Returns the GA4GH protocol representation of this ReferenceSet.
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ret = protocol.ReferenceSet()
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ret.description = pb.string(self.getDescription())
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train | AbstractReference.toProtocolElement | Returns the GA4GH protocol representation of this Reference. | ga4gh/server/datamodel/references.py | def toProtocolElement(self):
"""
Returns the GA4GH protocol representation of this Reference.
"""
reference = protocol.Reference()
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train | HtslibReference.populateFromRow | Populates this reference from the values in the specified DB row. | ga4gh/server/datamodel/references.py | def populateFromRow(self, referenceRecord):
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train | G2PUtility._extractAssociationsDetails | Given a set of results from our search query, return the
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Given a set of results from our search query, return the
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detailedURIRef = []
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train | G2PUtility._detailTuples | Given a list of uriRefs, return a list of dicts:
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train | G2PUtility._bindingsToDict | Given a binding from the sparql query result,
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train | G2PUtility._addDataFile | Given a filename, add it to the graph | ga4gh/server/datamodel/genotype_phenotype.py | def _addDataFile(self, filename):
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train | G2PUtility._getDetails | Given a uriRef, return a dict of all the details for that Ref
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train | G2PUtility._formatExternalIdentifiers | Formats several external identifiers for query | ga4gh/server/datamodel/genotype_phenotype.py | def _formatExternalIdentifiers(self, element, element_type):
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Formats several external identifiers for query
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elementClause = None
elements = []
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train | G2PUtility._formatExternalIdentifier | Formats a single external identifier for query | ga4gh/server/datamodel/genotype_phenotype.py | def _formatExternalIdentifier(self, element, element_type):
"""
Formats a single external identifier for query
"""
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term = "{}:{}".format(element['database'], element['identifier'])
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train | G2PUtility._formatOntologyTerm | Formats the ontology terms for query | ga4gh/server/datamodel/genotype_phenotype.py | def _formatOntologyTerm(self, element, element_type):
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Formats the ontology terms for query
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elementClause = None
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train | G2PUtility._formatOntologyTermObject | Formats the ontology term object for query | ga4gh/server/datamodel/genotype_phenotype.py | def _formatOntologyTermObject(self, terms, element_type):
"""
Formats the ontology term object for query
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elementClause = None
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terms = [terms]
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train | G2PUtility._formatIds | Formats a set of identifiers for query | ga4gh/server/datamodel/genotype_phenotype.py | def _formatIds(self, element, element_type):
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train | G2PUtility._formatEvidence | Formats elements passed into parts of a query for filtering | ga4gh/server/datamodel/genotype_phenotype.py | def _formatEvidence(self, elements):
"""
Formats elements passed into parts of a query for filtering
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elementClause = None
filters = []
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train | G2PUtility._toGA4GH | given an association dict,
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train | RdfPhenotypeAssociationSet._formatFilterQuery | Generate a formatted sparql query with appropriate filters | ga4gh/server/datamodel/genotype_phenotype.py | def _formatFilterQuery(self, request=None, featureSets=[]):
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train | RdfPhenotypeAssociationSet._filterSearchPhenotypesRequest | Filters request for phenotype search requests | ga4gh/server/datamodel/genotype_phenotype.py | def _filterSearchPhenotypesRequest(self, request):
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Filters request for phenotype search requests
"""
filters = []
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train | WiggleReader.wiggleFileHandleToProtocol | Return a continuous protocol object satsifiying the given query
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train | AbstractContinuousSet.toProtocolElement | Returns the representation of this ContinuousSet as the corresponding
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gaContinuousSet = protocol.ContinuousSet()
gaContinuousSet.id = self.getId()
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train | FileContinuousSet.populateFromRow | Populates the instance variables of this ContinuousSet from the
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Populates the instance variables of this ContinuousSet from the
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"""
self._filePath = continuousSetRecord.dataurl
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train | FileContinuousSet.getContinuous | 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 int, start position on reference
:param end: castable to int, end position on re... | ga4gh/server/datamodel/continuous.py | 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... | 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")
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train | SimulatedContinuousSet.getContinuousData | Returns a set number of simulated continuous data.
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:param start: start coordinate of query
:param end: end coordinate of query
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:param start: start coordinate of query
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:param start: start coordinate of query
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train | NetworkDriver.load_template | Will load a templated configuration on the device.
:param cls: Instance of the driver class.
:param template_name: Identifies the template name.
:param template_source (optional): Custom config template rendered and loaded on device
:param template_path (optional): Absolute path to dire... | napalm_base/base.py | def load_template(self, template_name, template_source=None,
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"""
Will load a templated configuration on the device.
:param cls: Instance of the driver class.
:param template_name: Identifies the template name.
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train | NetworkDriver.ping | Executes ping on the device and returns a dictionary with the result
:param destination: Host or IP Address of the destination
:param source (optional): Source address of echo request
:param ttl (optional): Maximum number of hops
:param timeout (optional): Maximum seconds to wait after ... | napalm_base/base.py | def ping(self, destination, source=c.PING_SOURCE, ttl=c.PING_TTL, timeout=c.PING_TIMEOUT,
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Executes ping on the device and returns a dictionary with the result
:param destination: Host or IP Address of the destination
... | def ping(self, destination, source=c.PING_SOURCE, ttl=c.PING_TTL, timeout=c.PING_TIMEOUT,
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train | MockDevice.run_commands | Only useful for EOS | napalm_base/mock.py | 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'") | def run_commands(self, commands):
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return list(self.parent.cli(commands).values())[0]
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raise AttributeError("MockedDriver instance has not attribute '_rpc'") | [
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train | textfsm_extractor | 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 the driver class
:param template_name: Specifies the name of t... | napalm_base/helpers.py | 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... | 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
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train | find_txt | 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 data.
:param default: Value to be returned in case ... | napalm_base/helpers.py | def find_txt(xml_tree, path, default=''):
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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'>.
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Extracts the text value from an XML tree, using XPath.
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train | convert | 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. | napalm_base/helpers.py | 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 ... | def convert(to, who, default=u''):
"""
Converts data to a specific datatype.
In case of error, will return a default value.
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:param who: value to cast.
:param default: value to return in case of error.
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train | mac | 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:AB'
Some vendors lik... | napalm_base/helpers.py | 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... | 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... | [
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train | compare_numeric | Compare numerical values. You can use '<%d','>%d'. | napalm_base/validate.py | 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)
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train | colon_separated_string_to_dict | 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 Mode VLAN: 1 (default)
Administrative Native VLAN tagging: disab... | napalm_base/utils/string_parsers.py | 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... | 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)
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