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train | AbstractFeatureSet.getCompoundIdForFeatureId | 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
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:return: string representing ID for the specified GA4GH protocol
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train | SimulatedFeatureSet.getFeature | Fetches a simulated feature by ID.
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train | SimulatedFeatureSet.getFeatures | Returns a set number of simulated features.
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train | Gff3DbFeatureSet.populateFromFile | Populates the instance variables of this FeatureSet from the specified
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Populates the instance variables of this FeatureSet from the specified
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train | Gff3DbFeatureSet.populateFromRow | Populates the instance variables of this FeatureSet from the specified
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Populates the instance variables of this FeatureSet from the specified
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train | Gff3DbFeatureSet.getFeature | Returns a protocol.Feature object corresponding to a compoundId
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train | Gff3DbFeatureSet._gaFeatureForFeatureDbRecord | :param feature: The DB Row representing a feature
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train | Gff3DbFeatureSet.getFeatures | method passed to runSearchRequest to fulfill the request
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train | AbstractRnaQuantificationSet.addRnaQuantification | Add an rnaQuantification to this rnaQuantificationSet | ga4gh/server/datamodel/rna_quantification.py | def addRnaQuantification(self, rnaQuantification):
"""
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train | AbstractRnaQuantificationSet.toProtocolElement | Converts this rnaQuant into its GA4GH protocol equivalent. | ga4gh/server/datamodel/rna_quantification.py | def toProtocolElement(self):
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train | SqliteRnaQuantificationSet.populateFromRow | Populates the instance variables of this RnaQuantificationSet from the
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train | AbstractRnaQuantification.toProtocolElement | Converts this rnaQuant into its GA4GH protocol equivalent. | ga4gh/server/datamodel/rna_quantification.py | def toProtocolElement(self):
"""
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train | AbstractRnaQuantification.addRnaQuantMetadata | data elements are:
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"""
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train | SqliteRnaQuantification.getRnaQuantMetadata | input is tab file with no header. Columns are:
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"""
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train | SqliteRnaQuantification.populateFromFile | Populates the instance variables of this FeatureSet from the specified
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"""
Populates the instance variables of this FeatureSet from the specified
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train | SqliteRnaQuantification.populateFromRow | Populates the instance variables of this FeatureSet from the specified
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"""
Populates the instance variables of this FeatureSet from the specified
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self._dbFilePath = row[b'dataUrl']
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train | SqliteRnaQuantification.getExpressionLevels | Returns the list of ExpressionLevels in this RNA Quantification. | ga4gh/server/datamodel/rna_quantification.py | def getExpressionLevels(
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"""
Returns the list of ExpressionLevels in this RNA Quantification.
"""
rnaQuantificationId = self.getLocalId()
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rnaQuantificationId = self.getLocalId()
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train | SqliteRnaBackend.searchRnaQuantificationsInDb | :param rnaQuantificationId: string restrict search by id
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train | SqliteRnaBackend.getRnaQuantificationById | :param rnaQuantificationId: the RNA Quantification ID
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train | SqliteRnaBackend.searchExpressionLevelsInDb | :param rnaQuantId: string restrict search by quantification id
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train | CallSet.populateFromRow | Populates this CallSet from the specified DB row. | ga4gh/server/datamodel/variants.py | def populateFromRow(self, callSetRecord):
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Populates this CallSet from the specified DB row.
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Populates this CallSet from the specified DB row.
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train | CallSet.toProtocolElement | Returns the representation of this CallSet as the corresponding
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Returns the representation of this CallSet as the corresponding
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"""
variantSet = self.getParentContainer()
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train | AbstractVariantSet.addVariantAnnotationSet | Adds the specified variantAnnotationSet to this dataset. | ga4gh/server/datamodel/variants.py | def addVariantAnnotationSet(self, variantAnnotationSet):
"""
Adds the specified variantAnnotationSet to this dataset.
"""
id_ = variantAnnotationSet.getId()
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train | AbstractVariantSet.getVariantAnnotationSet | Returns the AnnotationSet in this dataset with the specified 'id' | ga4gh/server/datamodel/variants.py | def getVariantAnnotationSet(self, id_):
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if id_ not in self._variantAnnotationSetIdMap:
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train | AbstractVariantSet.addCallSet | Adds the specfied CallSet to this VariantSet. | ga4gh/server/datamodel/variants.py | def addCallSet(self, callSet):
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Adds the specfied CallSet to this VariantSet.
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train | AbstractVariantSet.addCallSetFromName | Adds a CallSet for the specified sample name. | ga4gh/server/datamodel/variants.py | def addCallSetFromName(self, sampleName):
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Adds a CallSet for the specified sample name.
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callSet = CallSet(self, sampleName)
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train | AbstractVariantSet.getCallSetByName | Returns a CallSet with the specified name, or raises a
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"""
if name not in self._callSetNameMap:
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train | AbstractVariantSet.getCallSet | Returns a CallSet with the specified id, or raises a
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Returns a CallSet with the specified id, or raises a
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if id_ not in self._callSetIdMap:
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train | AbstractVariantSet.toProtocolElement | Converts this VariantSet into its GA4GH protocol equivalent. | ga4gh/server/datamodel/variants.py | 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... | def toProtocolElement(self):
"""
Converts this VariantSet into its GA4GH protocol equivalent.
"""
protocolElement = protocol.VariantSet()
protocolElement.id = self.getId()
protocolElement.dataset_id = self.getParentContainer().getId()
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train | AbstractVariantSet._createGaVariant | Convenience method to set the common fields in a GA Variant
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"""
Convenience method to set the common fields in a GA Variant
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"""
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Convenience method to set the common fields in a GA Variant
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train | AbstractVariantSet.getVariantId | Returns an ID string suitable for the specified GA Variant
object in this variant set. | ga4gh/server/datamodel/variants.py | 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(
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"""
Returns an ID string suitable for the specified GA Variant
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"""
md5 = self.hashVariant(gaVariant)
compoundId = datamodel.VariantCompoundId(
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train | AbstractVariantSet.getCallSetId | Returns the callSetId for the specified sampleName in this
VariantSet. | ga4gh/server/datamodel/variants.py | def getCallSetId(self, sampleName):
"""
Returns the callSetId for the specified sampleName in this
VariantSet.
"""
compoundId = datamodel.CallSetCompoundId(
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"""
Returns the callSetId for the specified sampleName in this
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"""
compoundId = datamodel.CallSetCompoundId(
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train | AbstractVariantSet.hashVariant | Produces an MD5 hash of the ga variant object to distinguish
it from other variants at the same genomic coordinate. | ga4gh/server/datamodel/variants.py | 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_... | 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))
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train | SimulatedVariantSet.generateVariant | 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. | ga4gh/server/datamodel/variants.py | 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... | def generateVariant(self, referenceName, position, randomNumberGenerator):
"""
Generate a random variant for the specified position using the
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train | HtslibVariantSet.populateFromRow | Populates this VariantSet from the specified DB row. | ga4gh/server/datamodel/variants.py | def populateFromRow(self, variantSetRecord):
"""
Populates this VariantSet from the specified DB row.
"""
self._created = variantSetRecord.created
self._updated = variantSetRecord.updated
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"""
Populates this VariantSet from the specified DB row.
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train | HtslibVariantSet.populateFromFile | 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. | ga4gh/server/datamodel/variants.py | def populateFromFile(self, dataUrls, indexFiles):
"""
Populates this variant set using the specified lists of data
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Populates this variant set using the specified lists of data
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train | HtslibVariantSet.populateFromDirectory | Populates this VariantSet by examing all the VCF files in the
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"""
Populates this VariantSet by examing all the VCF files in the
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Populates this VariantSet by examing all the VCF files in the
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train | HtslibVariantSet.checkConsistency | Perform consistency check on the variant set | ga4gh/server/datamodel/variants.py | 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:
... | def checkConsistency(self):
"""
Perform consistency check on the variant set
"""
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varFile = pysam.VariantFile(dataUrl, index_filename=indexFile)
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train | HtslibVariantSet._populateFromVariantFile | Populates the instance variables of this VariantSet from the specified
pysam VariantFile object. | ga4gh/server/datamodel/variants.py | def _populateFromVariantFile(self, varFile, dataUrl, indexFile):
"""
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"""
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"""
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train | HtslibVariantSet._updateVariantAnnotationSets | Updates the variant annotation set associated with this variant using
information in the specified pysam variantFile. | ga4gh/server/datamodel/variants.py | 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():
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"""
Updates the variant annotation set associated with this variant using
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# TODO check the consistency of this between VCF files.
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train | HtslibVariantSet._updateMetadata | Updates the metadata for his variant set based on the specified
variant file | ga4gh/server/datamodel/variants.py | 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 | def _updateMetadata(self, variantFile):
"""
Updates the metadata for his variant set based on the specified
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"""
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train | HtslibVariantSet._checkMetadata | Checks that metadata is consistent | ga4gh/server/datamodel/variants.py | def _checkMetadata(self, variantFile):
"""
Checks that metadata is consistent
"""
metadata = self._getMetadataFromVcf(variantFile)
if self._metadata is not None and self._metadata != metadata:
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train | HtslibVariantSet._checkCallSetIds | Checks callSetIds for consistency | ga4gh/server/datamodel/variants.py | def _checkCallSetIds(self, variantFile):
"""
Checks callSetIds for consistency
"""
if len(self._callSetIdMap) > 0:
callSetIds = set([
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for sample in variantFile.header.samples])
if callSetIds != set(self._ca... | def _checkCallSetIds(self, variantFile):
"""
Checks callSetIds for consistency
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train | HtslibVariantSet._updateCallSetIds | Updates the call set IDs based on the specified variant file. | ga4gh/server/datamodel/variants.py | def _updateCallSetIds(self, variantFile):
"""
Updates the call set IDs based on the specified variant file.
"""
if len(self._callSetIdMap) == 0:
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Updates the call set IDs based on the specified variant file.
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train | HtslibVariantSet.getPysamVariants | Returns an iterator over the pysam VCF records corresponding to the
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if referenceName in self._chromFileMap:
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train | HtslibVariantSet.getVariants | Returns an iterator over the specified variants. The parameters
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Returns the id of a metadata
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train | AbstractVariantAnnotationSet._createGaVariantAnnotation | Convenience method to set the common fields in a GA VariantAnnotation
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"""
Convenience method to set the common fields in a GA VariantAnnotation
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"""
ret = protocol.VariantAnnotation()
ret.created = self._creationTime
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"""
Convenience method to set the common fields in a GA VariantAnnotation
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train | AbstractVariantAnnotationSet.toProtocolElement | Converts this VariantAnnotationSet into its GA4GH protocol equivalent. | ga4gh/server/datamodel/variants.py | def toProtocolElement(self):
"""
Converts this VariantAnnotationSet into its GA4GH protocol equivalent.
"""
protocolElement = protocol.VariantAnnotationSet()
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train | AbstractVariantAnnotationSet.hashVariantAnnotation | Produces an MD5 hash of the gaVariant and gaVariantAnnotation objects | ga4gh/server/datamodel/variants.py | def hashVariantAnnotation(cls, gaVariant, gaVariantAnnotation):
"""
Produces an MD5 hash of the gaVariant and gaVariantAnnotation objects
"""
treffs = [treff.id for treff in gaVariantAnnotation.transcript_effects]
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"""
Produces an MD5 hash of the gaVariant and gaVariantAnnotation objects
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treffs = [treff.id for treff in gaVariantAnnotation.transcript_effects]
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train | AbstractVariantAnnotationSet.getVariantAnnotationId | Produces a stringified compoundId representing a variant
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:param gaAnnotation: protocol.VariantAnnotation
:return: compoundId String | ga4gh/server/datamodel/variants.py | def getVariantAnnotationId(self, gaVariant, gaAnnotation):
"""
Produces a stringified compoundId representing a variant
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:param gaAnnotation: protocol.VariantAnnotation
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:param gaAnnotation: protocol.VariantAnnotation
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train | HtslibVariantAnnotationSet.populateFromRow | Populates this VariantAnnotationSet from the specified DB row. | ga4gh/server/datamodel/variants.py | def populateFromRow(self, annotationSetRecord):
"""
Populates this VariantAnnotationSet from the specified DB row.
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train | HtslibVariantAnnotationSet._getAnnotationAnalysis | Assembles metadata within the VCF header into a GA4GH Analysis object.
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"""
Generator for iterating through variant annotations in this
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train | HtslibVariantAnnotationSet.convertLocationHgvsC | Accepts an annotation in HGVS notation and returns
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:param hgvsc:
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train | HtslibVariantAnnotationSet.addLocations | Adds locations to a GA4GH transcript effect object
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:param effect: protocol.TranscriptEffect
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"""
Adds locations to a GA4GH transcript effect object
by parsing HGVS annotation fields in concert with
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:param effect: protocol.TranscriptEffect
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Adds locations to a GA4GH transcript effect object
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Takes the ANN string of a SnpEff generated VCF, splits it
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train | HtslibVariantAnnotationSet.convertSeqOntology | Splits a string of sequence ontology effects and creates
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Splits a string of sequence ontology effects and creates
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Splits a string of sequence ontology effects and creates
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train | HtslibVariantAnnotationSet.convertVariantAnnotation | Converts the specfied pysam variant record into a GA4GH variant
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transcripts. | ga4gh/server/datamodel/variants.py | def convertVariantAnnotation(self, record):
"""
Converts the specfied pysam variant record into a GA4GH variant
annotation object using the specified function to convert the
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"""
variant = self._variantSet.convertVariant(record, [])
annotation = self._... | def convertVariantAnnotation(self, record):
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Converts the specfied pysam variant record into a GA4GH variant
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train | Feature._attributeStr | Return name=value for a single attribute | ga4gh/server/gff3.py | def _attributeStr(self, name):
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Return name=value for a single attribute
"""
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train | Feature._attributeStrs | Return name=value, semi-colon-separated string for attributes,
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"""
Return name=value, semi-colon-separated string for attributes,
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"""
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train | Feature.featureName | ID attribute from GFF3 or None if record doesn't have it.
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ID attribute from GFF3 or None if record doesn't have it.
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train | Gff3Set._linkFeature | Link a feature with its parents. | ga4gh/server/gff3.py | def _linkFeature(self, feature):
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Link a feature with its parents.
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parentNames = feature.attributes.get("Parent")
if parentNames is None:
self.roots.add(feature)
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train | Gff3Set._linkToParent | Link a feature with its children | ga4gh/server/gff3.py | def _linkToParent(self, feature, parentName):
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Link a feature with its children
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parentParts = self.byFeatureName.get(parentName)
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train | Gff3Set.linkChildFeaturesToParents | finish loading the set, constructing the tree | ga4gh/server/gff3.py | def linkChildFeaturesToParents(self):
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finish loading the set, constructing the tree
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# features maybe disjoint
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train | Gff3Set._recSortKey | Sort order for Features, by genomic coordinate,
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Sort order for Features, by genomic coordinate,
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train | Gff3Set._writeRec | Writes a single record to a file provided by the filehandle fh. | ga4gh/server/gff3.py | def _writeRec(self, fh, rec):
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Writes a single record to a file provided by the filehandle fh.
"""
fh.write(str(rec) + "\n")
for child in sorted(rec.children, key=self._recSortKey):
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train | Gff3Set.write | Write set to a GFF3 format file.
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"""
Write set to a GFF3 format file.
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fh.write(GFF3_HEADER+"\n")
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Write set to a GFF3 format file.
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train | Gff3Parser._open | open input file, optionally with decompression | ga4gh/server/gff3.py | def _open(self):
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open input file, optionally with decompression
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train | Gff3Parser._parseAttrs | Parse the attributes and values | ga4gh/server/gff3.py | def _parseAttrs(self, attrsStr):
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train | Gff3Parser._parseRecord | Parse one record. | ga4gh/server/gff3.py | def _parseRecord(self, gff3Set, line):
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train | AbstractDataRepository.addDataset | Adds the specified dataset to this data repository. | ga4gh/server/datarepo.py | def addDataset(self, dataset):
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Adds the specified dataset to this data repository.
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train | AbstractDataRepository.addOntology | Add an ontology map to this data repository. | ga4gh/server/datarepo.py | def addOntology(self, ontology):
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Add an ontology map to this data repository.
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train | AbstractDataRepository.getPeer | Select the first peer in the datarepo with the given url simulating
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train | AbstractDataRepository.getOntology | Returns the ontology with the specified ID. | ga4gh/server/datarepo.py | def getOntology(self, id_):
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Returns the ontology with the specified ID.
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train | AbstractDataRepository.getOntologyByName | Returns an ontology by name | ga4gh/server/datarepo.py | def getOntologyByName(self, name):
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Returns an ontology by name
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train | AbstractDataRepository.getReferenceSet | Retuns the ReferenceSet with the specified ID, or raises a
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Retuns the ReferenceSet with the specified ID, or raises a
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train | AbstractDataRepository.getReadGroupSet | Returns the readgroup set with the specified ID. | ga4gh/server/datarepo.py | def getReadGroupSet(self, id_):
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Returns the readgroup set with the specified ID.
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train | AbstractDataRepository.getVariantSet | Returns the readgroup set with the specified ID. | ga4gh/server/datarepo.py | def getVariantSet(self, id_):
"""
Returns the readgroup set with the specified ID.
"""
compoundId = datamodel.VariantSetCompoundId.parse(id_)
dataset = self.getDataset(compoundId.dataset_id)
return dataset.getVariantSet(id_) | def getVariantSet(self, id_):
"""
Returns the readgroup set with the specified ID.
"""
compoundId = datamodel.VariantSetCompoundId.parse(id_)
dataset = self.getDataset(compoundId.dataset_id)
return dataset.getVariantSet(id_) | [
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train | AbstractDataRepository.printSummary | Prints a summary of this data repository to stdout. | ga4gh/server/datarepo.py | def printSummary(self):
"""
Prints a summary of this data repository to stdout.
"""
print("Ontologies:")
for ontology in self.getOntologys():
print(
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ontology.getOntologyPrefix(),
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"""
Prints a summary of this data repository to stdout.
"""
print("Ontologies:")
for ontology in self.getOntologys():
print(
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train | AbstractDataRepository.allReadGroups | Return an iterator over all read groups in the data repo | ga4gh/server/datarepo.py | def allReadGroups(self):
"""
Return an iterator over all read groups in the data repo
"""
for dataset in self.getDatasets():
for readGroupSet in dataset.getReadGroupSets():
for readGroup in readGroupSet.getReadGroups():
yield readGroup | def allReadGroups(self):
"""
Return an iterator over all read groups in the data repo
"""
for dataset in self.getDatasets():
for readGroupSet in dataset.getReadGroupSets():
for readGroup in readGroupSet.getReadGroups():
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train | AbstractDataRepository.allFeatures | Return an iterator over all features in the data repo | ga4gh/server/datarepo.py | def allFeatures(self):
"""
Return an iterator over all features in the data repo
"""
for dataset in self.getDatasets():
for featureSet in dataset.getFeatureSets():
for feature in featureSet.getFeatures():
yield feature | def allFeatures(self):
"""
Return an iterator over all features in the data repo
"""
for dataset in self.getDatasets():
for featureSet in dataset.getFeatureSets():
for feature in featureSet.getFeatures():
yield feature | [
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train | AbstractDataRepository.allCallSets | Return an iterator over all call sets in the data repo | ga4gh/server/datarepo.py | def allCallSets(self):
"""
Return an iterator over all call sets in the data repo
"""
for dataset in self.getDatasets():
for variantSet in dataset.getVariantSets():
for callSet in variantSet.getCallSets():
yield callSet | def allCallSets(self):
"""
Return an iterator over all call sets in the data repo
"""
for dataset in self.getDatasets():
for variantSet in dataset.getVariantSets():
for callSet in variantSet.getCallSets():
yield callSet | [
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train | AbstractDataRepository.allVariantAnnotationSets | Return an iterator over all variant annotation sets
in the data repo | ga4gh/server/datarepo.py | def allVariantAnnotationSets(self):
"""
Return an iterator over all variant annotation sets
in the data repo
"""
for dataset in self.getDatasets():
for variantSet in dataset.getVariantSets():
for vaSet in variantSet.getVariantAnnotationSets():
... | def allVariantAnnotationSets(self):
"""
Return an iterator over all variant annotation sets
in the data repo
"""
for dataset in self.getDatasets():
for variantSet in dataset.getVariantSets():
for vaSet in variantSet.getVariantAnnotationSets():
... | [
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train | AbstractDataRepository.allRnaQuantifications | Return an iterator over all rna quantifications | ga4gh/server/datarepo.py | def allRnaQuantifications(self):
"""
Return an iterator over all rna quantifications
"""
for dataset in self.getDatasets():
for rnaQuantificationSet in dataset.getRnaQuantificationSets():
for rnaQuantification in \
rnaQuantificationSet.... | def allRnaQuantifications(self):
"""
Return an iterator over all rna quantifications
"""
for dataset in self.getDatasets():
for rnaQuantificationSet in dataset.getRnaQuantificationSets():
for rnaQuantification in \
rnaQuantificationSet.... | [
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] | ga4gh/ga4gh-server | python | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datarepo.py#L412-L420 | [
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train | AbstractDataRepository.allExpressionLevels | Return an iterator over all expression levels | ga4gh/server/datarepo.py | def allExpressionLevels(self):
"""
Return an iterator over all expression levels
"""
for dataset in self.getDatasets():
for rnaQuantificationSet in dataset.getRnaQuantificationSets():
for rnaQuantification in \
rnaQuantificationSet.getR... | def allExpressionLevels(self):
"""
Return an iterator over all expression levels
"""
for dataset in self.getDatasets():
for rnaQuantificationSet in dataset.getRnaQuantificationSets():
for rnaQuantification in \
rnaQuantificationSet.getR... | [
"Return",
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"all",
"expression",
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] | ga4gh/ga4gh-server | python | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datarepo.py#L422-L432 | [
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train | SqlDataRepository.getPeer | Finds a peer by URL and return the first peer record with that URL. | ga4gh/server/datarepo.py | def getPeer(self, url):
"""
Finds a peer by URL and return the first peer record with that URL.
"""
peers = list(models.Peer.select().where(models.Peer.url == url))
if len(peers) == 0:
raise exceptions.PeerNotFoundException(url)
return peers[0] | def getPeer(self, url):
"""
Finds a peer by URL and return the first peer record with that URL.
"""
peers = list(models.Peer.select().where(models.Peer.url == url))
if len(peers) == 0:
raise exceptions.PeerNotFoundException(url)
return peers[0] | [
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] | ga4gh/ga4gh-server | python | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datarepo.py#L528-L535 | [
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... | 1aa18922ef136db8604f6f098cb1732cba6f2a76 |
train | SqlDataRepository.getPeers | Get the list of peers using an SQL offset and limit. Returns a list
of peer datamodel objects in a list. | ga4gh/server/datarepo.py | def getPeers(self, offset=0, limit=1000):
"""
Get the list of peers using an SQL offset and limit. Returns a list
of peer datamodel objects in a list.
"""
select = models.Peer.select().order_by(
models.Peer.url).limit(limit).offset(offset)
return [peers.Peer(p... | def getPeers(self, offset=0, limit=1000):
"""
Get the list of peers using an SQL offset and limit. Returns a list
of peer datamodel objects in a list.
"""
select = models.Peer.select().order_by(
models.Peer.url).limit(limit).offset(offset)
return [peers.Peer(p... | [
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] | ga4gh/ga4gh-server | python | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datarepo.py#L537-L544 | [
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