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train | Backend.referenceSetsGenerator | Returns a generator over the (referenceSet, nextPageToken) pairs
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"""
Returns a generator over the (referenceSet, nextPageToken) pairs
defined by the specified request.
"""
results = []
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include = True
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train | Backend.referencesGenerator | Returns a generator over the (reference, nextPageToken) pairs
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"""
Returns a generator over the (reference, nextPageToken) pairs
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"""
referenceSet = self.getDataRepository().getReferenceSet(
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train | Backend.variantSetsGenerator | Returns a generator over the (variantSet, nextPageToken) pairs defined
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Returns a generator over the (variantSet, nextPageToken) pairs defined
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train | Backend.variantAnnotationSetsGenerator | Returns a generator over the (variantAnnotationSet, nextPageToken)
pairs defined by the specified request. | ga4gh/server/backend.py | def variantAnnotationSetsGenerator(self, request):
"""
Returns a generator over the (variantAnnotationSet, nextPageToken)
pairs defined by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
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dataset = self.getD... | def variantAnnotationSetsGenerator(self, request):
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train | Backend.readsGenerator | Returns a generator over the (read, nextPageToken) pairs defined
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"""
Returns a generator over the (read, nextPageToken) pairs defined
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"""
if not request.reference_id:
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if len(request.read_group_ids) < 1:
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train | Backend.variantsGenerator | Returns a generator over the (variant, nextPageToken) pairs defined
by the specified request. | ga4gh/server/backend.py | def variantsGenerator(self, request):
"""
Returns a generator over the (variant, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId \
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train | Backend.variantAnnotationsGenerator | Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
defined by the specified request. | ga4gh/server/backend.py | def variantAnnotationsGenerator(self, request):
"""
Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
defined by the specified request.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(
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dat... | def variantAnnotationsGenerator(self, request):
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Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
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train | Backend.featuresGenerator | Returns a generator over the (features, nextPageToken) pairs
defined by the (JSON string) request. | ga4gh/server/backend.py | def featuresGenerator(self, request):
"""
Returns a generator over the (features, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
parentId = None
if request.feature_set_id != "":
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train | Backend.continuousGenerator | Returns a generator over the (continuous, nextPageToken) pairs
defined by the (JSON string) request. | ga4gh/server/backend.py | def continuousGenerator(self, request):
"""
Returns a generator over the (continuous, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
if request.continuous_set_id != "":
compoundId = datamodel.ContinuousSetCompoundId.parse(
... | def continuousGenerator(self, request):
"""
Returns a generator over the (continuous, nextPageToken) pairs
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"""
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train | Backend.phenotypesGenerator | Returns a generator over the (phenotypes, nextPageToken) pairs
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"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
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train | Backend.genotypesPhenotypesGenerator | Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request | ga4gh/server/backend.py | def genotypesPhenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
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train | Backend.callSetsGenerator | Returns a generator over the (callSet, nextPageToken) pairs defined
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"""
Returns a generator over the (callSet, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
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dataset = self.getDataRepository().getDataset... | def callSetsGenerator(self, request):
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"""
Returns a generator over the (featureSet, nextPageToken) pairs
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dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
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train | Backend.continuousSetsGenerator | Returns a generator over the (continuousSet, nextPageToken) pairs
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"""
Returns a generator over the (continuousSet, nextPageToken) pairs
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"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
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train | Backend.rnaQuantificationSetsGenerator | Returns a generator over the (rnaQuantificationSet, nextPageToken)
pairs defined by the specified request. | ga4gh/server/backend.py | def rnaQuantificationSetsGenerator(self, request):
"""
Returns a generator over the (rnaQuantificationSet, nextPageToken)
pairs defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
... | def rnaQuantificationSetsGenerator(self, request):
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dataset = self.getDataRepository().getDataset(request.dataset_id)
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train | Backend.rnaQuantificationsGenerator | Returns a generator over the (rnaQuantification, nextPageToken) pairs
defined by the specified request. | ga4gh/server/backend.py | def rnaQuantificationsGenerator(self, request):
"""
Returns a generator over the (rnaQuantification, nextPageToken) pairs
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"""
if len(request.rna_quantification_set_id) < 1:
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Returns a generator over the (rnaQuantification, nextPageToken) pairs
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train | Backend.expressionLevelsGenerator | Returns a generator over the (expressionLevel, nextPageToken) pairs
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Returns a generator over the (expressionLevel, nextPageToken) pairs
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"""
rnaQuantificationId = request.rna_quantificati... | def expressionLevelsGenerator(self, request):
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"""
Runs a get request by converting the specified datamodel
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"""
protocolElement = obj.toProtocolElement()
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train | Backend.runListReferenceBases | Runs a listReferenceBases request for the specified ID and
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"""
Runs a listReferenceBases request for the specified ID and
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"""
# In the case when an empty post request is made to the endpoint
# we instantiate an empty ListReferenceBasesRequest.
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Runs a listReferenceBases request for the specified ID and
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Returns a callset with the given id
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compoundId = datamodel.CallSetCompoundId.parse(id_)
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variantSet = dataset.getVariantSet(compoundId.variant_set_id)
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"""
Returns a callset with the given id
"""
compoundId = datamodel.CallSetCompoundId.parse(id_)
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train | Backend.runGetInfo | Returns information about the service including protocol version. | ga4gh/server/backend.py | def runGetInfo(self, request):
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Returns information about the service including protocol version.
"""
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Returns information about the service including protocol version.
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train | Backend.runAddAnnouncement | Takes a flask request from the frontend and attempts to parse
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"""
Takes a flask request from the frontend and attempts to parse
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announcement to the `announcement` table with some other metadata
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train | Backend.runListPeers | Takes a ListPeersRequest and returns a ListPeersResponse using
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"""
Takes a ListPeersRequest and returns a ListPeersResponse using
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"""
return self.runSearchRequest(
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... | def runListPeers(self, request):
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Takes a ListPeersRequest and returns a ListPeersResponse using
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train | Backend.runGetVariant | Returns a variant with the given id | ga4gh/server/backend.py | def runGetVariant(self, id_):
"""
Returns a variant with the given id
"""
compoundId = datamodel.VariantCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
gaVaria... | def runGetVariant(self, id_):
"""
Returns a variant with the given id
"""
compoundId = datamodel.VariantCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
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train | Backend.runGetBiosample | Runs a getBiosample request for the specified ID. | ga4gh/server/backend.py | def runGetBiosample(self, id_):
"""
Runs a getBiosample request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
biosample = dataset.getBiosample(id_)
return self.r... | def runGetBiosample(self, id_):
"""
Runs a getBiosample request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
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train | Backend.runGetIndividual | Runs a getIndividual request for the specified ID. | ga4gh/server/backend.py | def runGetIndividual(self, id_):
"""
Runs a getIndividual request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
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train | Backend.runGetFeature | Returns JSON string of the feature object corresponding to
the feature compoundID passed in. | ga4gh/server/backend.py | def runGetFeature(self, id_):
"""
Returns JSON string of the feature object corresponding to
the feature compoundID passed in.
"""
compoundId = datamodel.FeatureCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
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Returns JSON string of the feature object corresponding to
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train | Backend.runGetReadGroupSet | Returns a readGroupSet with the given id_ | ga4gh/server/backend.py | def runGetReadGroupSet(self, id_):
"""
Returns a readGroupSet with the given id_
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(id_)
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train | Backend.runGetReadGroup | Returns a read group with the given id_ | ga4gh/server/backend.py | def runGetReadGroup(self, id_):
"""
Returns a read group with the given id_
"""
compoundId = datamodel.ReadGroupCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
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"""
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dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
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train | Backend.runGetReference | Runs a getReference request for the specified ID. | ga4gh/server/backend.py | def runGetReference(self, id_):
"""
Runs a getReference request for the specified ID.
"""
compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getDataRepository().getReferenceSet(
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reference = referenceSet.getRe... | def runGetReference(self, id_):
"""
Runs a getReference request for the specified ID.
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compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getDataRepository().getReferenceSet(
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"""
referenceSet = self.getDataRepository().getReferenceSet(id_)
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train | Backend.runGetVariantSet | Runs a getVariantSet request for the specified ID. | ga4gh/server/backend.py | def runGetVariantSet(self, id_):
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train | Backend.runGetFeatureSet | Runs a getFeatureSet request for the specified ID. | ga4gh/server/backend.py | def runGetFeatureSet(self, id_):
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Runs a getFeatureSet request for the specified ID.
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train | Backend.runGetContinuousSet | Runs a getContinuousSet request for the specified ID. | ga4gh/server/backend.py | def runGetContinuousSet(self, id_):
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train | Backend.runGetDataset | Runs a getDataset request for the specified ID. | ga4gh/server/backend.py | def runGetDataset(self, id_):
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train | Backend.runGetRnaQuantification | Runs a getRnaQuantification request for the specified ID. | ga4gh/server/backend.py | def runGetRnaQuantification(self, id_):
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Runs a getRnaQuantification request for the specified ID.
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compoundId = datamodel.RnaQuantificationCompoundId.parse(id_)
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train | Backend.runGetRnaQuantificationSet | Runs a getRnaQuantificationSet request for the specified ID. | ga4gh/server/backend.py | def runGetRnaQuantificationSet(self, id_):
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train | Backend.runGetExpressionLevel | Runs a getExpressionLevel request for the specified ID. | ga4gh/server/backend.py | def runGetExpressionLevel(self, id_):
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Runs a getExpressionLevel request for the specified ID.
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compoundId = datamodel.ExpressionLevelCompoundId.parse(id_)
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train | Backend.runSearchReadGroupSets | Runs the specified SearchReadGroupSetsRequest. | ga4gh/server/backend.py | def runSearchReadGroupSets(self, request):
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Runs the specified SearchReadGroupSetsRequest.
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train | Backend.runSearchIndividuals | Runs the specified search SearchIndividualsRequest. | ga4gh/server/backend.py | def runSearchIndividuals(self, request):
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Runs the specified search SearchIndividualsRequest.
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train | Backend.runSearchBiosamples | Runs the specified SearchBiosamplesRequest. | ga4gh/server/backend.py | def runSearchBiosamples(self, request):
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Runs the specified SearchBiosamplesRequest.
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return self.runSearchRequest(
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train | Backend.runSearchReads | Runs the specified SearchReadsRequest. | ga4gh/server/backend.py | def runSearchReads(self, request):
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Runs the specified SearchReadsRequest.
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train | Backend.runSearchReferenceSets | Runs the specified SearchReferenceSetsRequest. | ga4gh/server/backend.py | def runSearchReferenceSets(self, request):
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Runs the specified SearchReferenceSetsRequest.
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train | Backend.runSearchReferences | Runs the specified SearchReferenceRequest. | ga4gh/server/backend.py | def runSearchReferences(self, request):
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train | Backend.runSearchVariantSets | Runs the specified SearchVariantSetsRequest. | ga4gh/server/backend.py | def runSearchVariantSets(self, request):
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Runs the specified SearchVariantSetsRequest.
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train | Backend.runSearchVariantAnnotationSets | Runs the specified SearchVariantAnnotationSetsRequest. | ga4gh/server/backend.py | def runSearchVariantAnnotationSets(self, request):
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Runs the specified SearchVariantAnnotationSetsRequest.
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train | Backend.runSearchVariants | Runs the specified SearchVariantRequest. | ga4gh/server/backend.py | def runSearchVariants(self, request):
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Runs the specified SearchVariantRequest.
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return self.runSearchRequest(
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train | Backend.runSearchVariantAnnotations | Runs the specified SearchVariantAnnotationsRequest. | ga4gh/server/backend.py | def runSearchVariantAnnotations(self, request):
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train | Backend.runSearchCallSets | Runs the specified SearchCallSetsRequest. | ga4gh/server/backend.py | def runSearchCallSets(self, request):
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train | Backend.runSearchDatasets | Runs the specified SearchDatasetsRequest. | ga4gh/server/backend.py | def runSearchDatasets(self, request):
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Runs the specified SearchDatasetsRequest.
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train | Backend.runSearchFeatureSets | Returns a SearchFeatureSetsResponse for the specified
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train | Backend.runSearchFeatures | Returns a SearchFeaturesResponse for the specified
SearchFeaturesRequest object.
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Returns a SearchFeaturesResponse for the specified
SearchFeaturesRequest object.
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train | Backend.runSearchContinuousSets | Returns a SearchContinuousSetsResponse for the specified
SearchContinuousSetsRequest object. | ga4gh/server/backend.py | def runSearchContinuousSets(self, request):
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SearchContinuousSetsRequest object.
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train | Backend.runSearchContinuous | Returns a SearchContinuousResponse for the specified
SearchContinuousRequest object.
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Returns a SearchContinuousResponse for the specified
SearchContinuousRequest object.
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train | Backend.runSearchRnaQuantificationSets | Returns a SearchRnaQuantificationSetsResponse for the specified
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Returns a SearchRnaQuantificationSetsResponse for the specified
SearchRnaQuantificationSetsRequest object.
"""
return self.runSearchRequest(
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train | Backend.runSearchRnaQuantifications | Returns a SearchRnaQuantificationResponse for the specified
SearchRnaQuantificationRequest object. | ga4gh/server/backend.py | def runSearchRnaQuantifications(self, request):
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Returns a SearchRnaQuantificationResponse for the specified
SearchRnaQuantificationRequest object.
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return self.runSearchRequest(
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train | Backend.runSearchExpressionLevels | Returns a SearchExpressionLevelResponse for the specified
SearchExpressionLevelRequest object. | ga4gh/server/backend.py | def runSearchExpressionLevels(self, request):
"""
Returns a SearchExpressionLevelResponse for the specified
SearchExpressionLevelRequest object.
"""
return self.runSearchRequest(
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protocol.SearchExpressionLev... | def runSearchExpressionLevels(self, request):
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Returns a SearchExpressionLevelResponse for the specified
SearchExpressionLevelRequest object.
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train | Dataset.populateFromRow | Populates the instance variables of this Dataset from the
specified database row. | ga4gh/server/datamodel/datasets.py | def populateFromRow(self, dataset):
"""
Populates the instance variables of this Dataset from the
specified database row.
"""
self._description = dataset.description
self.setAttributesJson(dataset.attributes) | def populateFromRow(self, dataset):
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Populates the instance variables of this Dataset from the
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train | Dataset.addVariantSet | Adds the specified variantSet to this dataset. | ga4gh/server/datamodel/datasets.py | def addVariantSet(self, variantSet):
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Adds the specified variantSet to this dataset.
"""
id_ = variantSet.getId()
self._variantSetIdMap[id_] = variantSet
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Adds the specified variantSet to this dataset.
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train | Dataset.addBiosample | Adds the specified biosample to this dataset. | ga4gh/server/datamodel/datasets.py | def addBiosample(self, biosample):
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Adds the specified biosample to this dataset.
"""
id_ = biosample.getId()
self._biosampleIdMap[id_] = biosample
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Adds the specified biosample to this dataset.
"""
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train | Dataset.addIndividual | Adds the specified individual to this dataset. | ga4gh/server/datamodel/datasets.py | def addIndividual(self, individual):
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Adds the specified individual to this dataset.
"""
id_ = individual.getId()
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Adds the specified individual to this dataset.
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train | Dataset.addFeatureSet | Adds the specified featureSet to this dataset. | ga4gh/server/datamodel/datasets.py | def addFeatureSet(self, featureSet):
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Adds the specified featureSet to this dataset.
"""
id_ = featureSet.getId()
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train | Dataset.addContinuousSet | Adds the specified continuousSet to this dataset. | ga4gh/server/datamodel/datasets.py | def addContinuousSet(self, continuousSet):
"""
Adds the specified continuousSet to this dataset.
"""
id_ = continuousSet.getId()
self._continuousSetIdMap[id_] = continuousSet
self._continuousSetIds.append(id_)
name = continuousSet.getLocalId()
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Adds the specified continuousSet to this dataset.
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id_ = continuousSet.getId()
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train | Dataset.addReadGroupSet | Adds the specified readGroupSet to this dataset. | ga4gh/server/datamodel/datasets.py | def addReadGroupSet(self, readGroupSet):
"""
Adds the specified readGroupSet to this dataset.
"""
id_ = readGroupSet.getId()
self._readGroupSetIdMap[id_] = readGroupSet
self._readGroupSetNameMap[readGroupSet.getLocalId()] = readGroupSet
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"""
Adds the specified readGroupSet to this dataset.
"""
id_ = readGroupSet.getId()
self._readGroupSetIdMap[id_] = readGroupSet
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train | Dataset.addRnaQuantificationSet | Adds the specified rnaQuantification set to this dataset. | ga4gh/server/datamodel/datasets.py | def addRnaQuantificationSet(self, rnaQuantSet):
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train | Dataset.getVariantSetByName | Returns a VariantSet with the specified name, or raises a
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train | Dataset.addPhenotypeAssociationSet | Adds the specified g2p association set to this backend. | ga4gh/server/datamodel/datasets.py | def addPhenotypeAssociationSet(self, phenotypeAssociationSet):
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Adds the specified g2p association set to this backend.
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train | Dataset.getFeatureSet | Returns the FeatureSet with the specified id, or raises a
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train | Dataset.getFeatureSetByName | Returns the FeatureSet with the specified name, or raises
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train | Dataset.getContinuousSet | Returns the ContinuousSet with the specified id, or raises a
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train | Dataset.getContinuousSetByName | Returns the ContinuousSet with the specified name, or raises
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train | Dataset.getBiosampleByName | Returns a Biosample with the specified name, or raises a
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train | Dataset.getIndividualByName | Returns an individual with the specified name, or raises a
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train | Dataset.getIndividual | Returns the Individual with the specified id, or raises
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if id_ not in self._individualIdMap:
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train | Dataset.getReadGroupSetByName | Returns a ReadGroupSet with the specified name, or raises a
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train | Dataset.getRnaQuantificationSetByName | Returns the RnaQuantification set with the specified name, or raises
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train | AlignmentDataMixin.convertReadAlignment | Convert a pysam ReadAlignment to a GA4GH ReadAlignment | ga4gh/server/datamodel/reads.py | def convertReadAlignment(self, read, readGroupSet, readGroupId):
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# TODO fill out remaining fields
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Adds the specified ReadGroup to this ReadGroupSet.
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Returns the ReadGroup with the specified id if it exists in this
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"""
Returns the GA4GH protocol representation of this ReadGroupSet.
"""
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Returns the GA4GH protocol representation of this ReadGroupSet.
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train | AbstractReadGroupSet.getReadAlignmentId | Returns a string ID suitable for use in the specified GA
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"""
Returns a string ID suitable for use in the specified GA
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"""
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Returns the GA4GH protocol representation of this read group set's
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"""
Populates the instance variables of this ReadGroupSet from the
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Returns the GA4GH protocol representation of this ReadGroup.
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Returns the GA4GH protocol representation of this read group's
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"""
stats = protocol.ReadStats()
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stats.unaligned_read_count = self.getNumUnalignedReads()
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train | AbstractReadGroup.getExperiment | Returns the GA4GH protocol representation of this read group's
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"""
Returns the GA4GH protocol representation of this read group's
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"""
experiment = protocol.Experiment()
experiment.id = self.getExperimentId()
experiment.instrument_model = pb.string(self.getInstrumentModel())
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train | HtslibReadGroup.populateFromHeader | Populate the instance variables using the specified SAM header. | ga4gh/server/datamodel/reads.py | def populateFromHeader(self, readGroupHeader):
"""
Populate the instance variables using the specified SAM header.
"""
self._sampleName = readGroupHeader.get('SM', None)
self._description = readGroupHeader.get('DS', None)
if 'PI' in readGroupHeader:
self._pred... | def populateFromHeader(self, readGroupHeader):
"""
Populate the instance variables using the specified SAM header.
"""
self._sampleName = readGroupHeader.get('SM', None)
self._description = readGroupHeader.get('DS', None)
if 'PI' in readGroupHeader:
self._pred... | [
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] | ga4gh/ga4gh-server | python | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/reads.py#L741-L754 | [
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train | HtslibReadGroup.populateFromRow | Populate the instance variables using the specified DB row. | ga4gh/server/datamodel/reads.py | def populateFromRow(self, readGroupRecord):
"""
Populate the instance variables using the specified DB row.
"""
self._sampleName = readGroupRecord.samplename
self._biosampleId = readGroupRecord.biosampleid
self._description = readGroupRecord.description
self._pred... | def populateFromRow(self, readGroupRecord):
"""
Populate the instance variables using the specified DB row.
"""
self._sampleName = readGroupRecord.samplename
self._biosampleId = readGroupRecord.biosampleid
self._description = readGroupRecord.description
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] | ga4gh/ga4gh-server | python | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/reads.py#L756-L774 | [
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train | getNameFromPath | Returns the filename of the specified path without its extensions.
This is usually how we derive the default name for a given object. | ga4gh/server/cli/repomanager.py | def getNameFromPath(filePath):
"""
Returns the filename of the specified path without its extensions.
This is usually how we derive the default name for a given object.
"""
if len(filePath) == 0:
raise ValueError("Cannot have empty path for name")
fileName = os.path.split(os.path.normpat... | def getNameFromPath(filePath):
"""
Returns the filename of the specified path without its extensions.
This is usually how we derive the default name for a given object.
"""
if len(filePath) == 0:
raise ValueError("Cannot have empty path for name")
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... | 1aa18922ef136db8604f6f098cb1732cba6f2a76 |
train | repoExitError | Exits the repo manager with error status. | ga4gh/server/cli/repomanager.py | def repoExitError(message):
"""
Exits the repo manager with error status.
"""
wrapper = textwrap.TextWrapper(
break_on_hyphens=False, break_long_words=False)
formatted = wrapper.fill("{}: error: {}".format(sys.argv[0], message))
sys.exit(formatted) | def repoExitError(message):
"""
Exits the repo manager with error status.
"""
wrapper = textwrap.TextWrapper(
break_on_hyphens=False, break_long_words=False)
formatted = wrapper.fill("{}: error: {}".format(sys.argv[0], message))
sys.exit(formatted) | [
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] | ga4gh/ga4gh-server | python | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/cli/repomanager.py#L1206-L1213 | [
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