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def isUrl(urlString):
""" Attempts to return whether a given URL string is valid by checking for the presence of the URL scheme and netloc using the urlparse module, and then using a regex. From http://stackoverflow.com/questions/7160737/ """ |
parsed = urlparse.urlparse(urlString)
urlparseValid = parsed.netloc != '' and parsed.scheme != ''
regex = re.compile(
r'^(?:http|ftp)s?://' # http:// or https://
r'(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)'
r'+(?:[A-Z]{2,6}\.?|[A-Z0-9-]{2,}\.?)|' # domain...
r'localhost|' # localhost...
r'\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3})' # ...or ip
r'(?::\d+)?' # optional port
r'(?:/?|[/?]\S+)$', re.IGNORECASE)
return regex.match(urlString) and urlparseValid |
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def setUrl(self, url):
""" Attempt to safely set the URL by string. """ |
if isUrl(url):
self._url = url
else:
raise exceptions.BadUrlException(url)
return self |
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def setAttributesJson(self, attributesJson):
""" Sets the attributes dictionary from a JSON string. """ |
try:
self._attributes = json.loads(attributesJson)
except:
raise exceptions.InvalidJsonException(attributesJson)
return self |
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def populateFromRow(self, peerRecord):
""" This method accepts a model record and sets class variables. """ |
self.setUrl(peerRecord.url) \
.setAttributesJson(peerRecord.attributes)
return self |
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def _protocolListGenerator(self, request, objectList):
""" Returns a generator over the objects in the specified list using _protocolObjectGenerator to generate page tokens. """ |
return self._protocolObjectGenerator(
request, len(objectList), lambda index: objectList[index]) |
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def _objectListGenerator(self, request, objectList):
""" Returns a generator over the objects in the specified list using _topLevelObjectGenerator to generate page tokens. """ |
return self._topLevelObjectGenerator(
request, len(objectList), lambda index: objectList[index]) |
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def runGetRequest(self, obj):
""" Runs a get request by converting the specified datamodel object into its protocol representation. """ |
protocolElement = obj.toProtocolElement()
jsonString = protocol.toJson(protocolElement)
return jsonString |
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def runListReferenceBases(self, requestJson):
""" Runs a listReferenceBases request for the specified ID and request arguments. """ |
# In the case when an empty post request is made to the endpoint
# we instantiate an empty ListReferenceBasesRequest.
if not requestJson:
request = protocol.ListReferenceBasesRequest()
else:
try:
request = protocol.fromJson(
requestJson,
protocol.ListReferenceBasesRequest)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestJson)
compoundId = datamodel.ReferenceCompoundId.parse(request.reference_id)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(request.reference_id)
start = request.start
end = request.end
if end == 0: # assume meant "get all"
end = reference.getLength()
if request.page_token:
pageTokenStr = request.page_token
start = paging._parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
nextPageToken = None
if start + chunkSize < end:
end = start + chunkSize
nextPageToken = str(start + chunkSize)
sequence = reference.getBases(start, end)
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
if nextPageToken:
response.next_page_token = nextPageToken
return protocol.toJson(response) |
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def runGetCallSet(self, id_):
""" Returns a callset with the given id """ |
compoundId = datamodel.CallSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
callSet = variantSet.getCallSet(id_)
return self.runGetRequest(callSet) |
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def runGetInfo(self, request):
""" Returns information about the service including protocol version. """ |
return protocol.toJson(protocol.GetInfoResponse(
protocol_version=protocol.version)) |
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def runAddAnnouncement(self, flaskrequest):
""" Takes a flask request from the frontend and attempts to parse into an AnnouncePeerRequest. If successful, it will log the announcement to the `announcement` table with some other metadata gathered from the request. """ |
announcement = {}
# We want to parse the request ourselves to collect a little more
# data about it.
try:
requestData = protocol.fromJson(
flaskrequest.get_data(), protocol.AnnouncePeerRequest)
announcement['hostname'] = flaskrequest.host_url
announcement['remote_addr'] = flaskrequest.remote_addr
announcement['user_agent'] = flaskrequest.headers.get('User-Agent')
except AttributeError:
# Sometimes in testing we will send protocol requests instead
# of flask requests and so the hostname and user agent won't
# be present.
try:
requestData = protocol.fromJson(
flaskrequest, protocol.AnnouncePeerRequest)
except Exception as e:
raise exceptions.InvalidJsonException(e)
except Exception as e:
raise exceptions.InvalidJsonException(e)
# Validate the url before accepting the announcement
peer = datamodel.peers.Peer(requestData.peer.url)
peer.setAttributesJson(protocol.toJson(
requestData.peer.attributes))
announcement['url'] = peer.getUrl()
announcement['attributes'] = peer.getAttributes()
try:
self.getDataRepository().insertAnnouncement(announcement)
except:
raise exceptions.BadRequestException(announcement['url'])
return protocol.toJson(
protocol.AnnouncePeerResponse(success=True)) |
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def runListPeers(self, request):
""" Takes a ListPeersRequest and returns a ListPeersResponse using a page_token and page_size if provided. """ |
return self.runSearchRequest(
request,
protocol.ListPeersRequest,
protocol.ListPeersResponse,
self.peersGenerator) |
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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)
gaVariant = variantSet.getVariant(compoundId)
# TODO variant is a special case here, as it's returning a
# protocol element rather than a datamodel object. We should
# fix this for consistency.
jsonString = protocol.toJson(gaVariant)
return jsonString |
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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.runGetRequest(biosample) |
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def runGetIndividual(self, id_):
""" Runs a getIndividual request for the specified ID. """ |
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
individual = dataset.getIndividual(id_)
return self.runGetRequest(individual) |
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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)
featureSet = dataset.getFeatureSet(compoundId.feature_set_id)
gaFeature = featureSet.getFeature(compoundId)
jsonString = protocol.toJson(gaFeature)
return jsonString |
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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_)
return self.runGetRequest(readGroupSet) |
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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)
readGroup = readGroupSet.getReadGroup(id_)
return self.runGetRequest(readGroup) |
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def runGetReference(self, id_):
""" Runs a getReference request for the specified ID. """ |
compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(id_)
return self.runGetRequest(reference) |
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def runGetReferenceSet(self, id_):
""" Runs a getReferenceSet request for the specified ID. """ |
referenceSet = self.getDataRepository().getReferenceSet(id_)
return self.runGetRequest(referenceSet) |
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def runGetFeatureSet(self, id_):
""" Runs a getFeatureSet request for the specified ID. """ |
compoundId = datamodel.FeatureSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
featureSet = dataset.getFeatureSet(id_)
return self.runGetRequest(featureSet) |
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def runGetContinuousSet(self, id_):
""" Runs a getContinuousSet request for the specified ID. """ |
compoundId = datamodel.ContinuousSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
continuousSet = dataset.getContinuousSet(id_)
return self.runGetRequest(continuousSet) |
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def runGetDataset(self, id_):
""" Runs a getDataset request for the specified ID. """ |
dataset = self.getDataRepository().getDataset(id_)
return self.runGetRequest(dataset) |
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def runGetRnaQuantification(self, id_):
""" Runs a getRnaQuantification request for the specified ID. """ |
compoundId = datamodel.RnaQuantificationCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(id_)
return self.runGetRequest(rnaQuantification) |
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def runGetRnaQuantificationSet(self, id_):
""" Runs a getRnaQuantificationSet request for the specified ID. """ |
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(id_)
return self.runGetRequest(rnaQuantificationSet) |
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def runGetExpressionLevel(self, id_):
""" Runs a getExpressionLevel request for the specified ID. """ |
compoundId = datamodel.ExpressionLevelCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(
compoundId.rna_quantification_id)
expressionLevel = rnaQuantification.getExpressionLevel(compoundId)
return self.runGetRequest(expressionLevel) |
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def runSearchReadGroupSets(self, request):
""" Runs the specified SearchReadGroupSetsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchReadGroupSetsRequest,
protocol.SearchReadGroupSetsResponse,
self.readGroupSetsGenerator) |
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def runSearchIndividuals(self, request):
""" Runs the specified search SearchIndividualsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchIndividualsRequest,
protocol.SearchIndividualsResponse,
self.individualsGenerator) |
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def runSearchBiosamples(self, request):
""" Runs the specified SearchBiosamplesRequest. """ |
return self.runSearchRequest(
request, protocol.SearchBiosamplesRequest,
protocol.SearchBiosamplesResponse,
self.biosamplesGenerator) |
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def runSearchReads(self, request):
""" Runs the specified SearchReadsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchReadsRequest,
protocol.SearchReadsResponse,
self.readsGenerator) |
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def runSearchReferenceSets(self, request):
""" Runs the specified SearchReferenceSetsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchReferenceSetsRequest,
protocol.SearchReferenceSetsResponse,
self.referenceSetsGenerator) |
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def runSearchReferences(self, request):
""" Runs the specified SearchReferenceRequest. """ |
return self.runSearchRequest(
request, protocol.SearchReferencesRequest,
protocol.SearchReferencesResponse,
self.referencesGenerator) |
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def runSearchVariantSets(self, request):
""" Runs the specified SearchVariantSetsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchVariantSetsRequest,
protocol.SearchVariantSetsResponse,
self.variantSetsGenerator) |
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def runSearchVariantAnnotationSets(self, request):
""" Runs the specified SearchVariantAnnotationSetsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchVariantAnnotationSetsRequest,
protocol.SearchVariantAnnotationSetsResponse,
self.variantAnnotationSetsGenerator) |
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def runSearchVariants(self, request):
""" Runs the specified SearchVariantRequest. """ |
return self.runSearchRequest(
request, protocol.SearchVariantsRequest,
protocol.SearchVariantsResponse,
self.variantsGenerator) |
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def runSearchVariantAnnotations(self, request):
""" Runs the specified SearchVariantAnnotationsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchVariantAnnotationsRequest,
protocol.SearchVariantAnnotationsResponse,
self.variantAnnotationsGenerator) |
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def runSearchCallSets(self, request):
""" Runs the specified SearchCallSetsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchCallSetsRequest,
protocol.SearchCallSetsResponse,
self.callSetsGenerator) |
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def runSearchDatasets(self, request):
""" Runs the specified SearchDatasetsRequest. """ |
return self.runSearchRequest(
request, protocol.SearchDatasetsRequest,
protocol.SearchDatasetsResponse,
self.datasetsGenerator) |
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def runSearchFeatureSets(self, request):
""" Returns a SearchFeatureSetsResponse for the specified SearchFeatureSetsRequest object. """ |
return self.runSearchRequest(
request, protocol.SearchFeatureSetsRequest,
protocol.SearchFeatureSetsResponse,
self.featureSetsGenerator) |
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def runSearchFeatures(self, request):
""" Returns a SearchFeaturesResponse for the specified SearchFeaturesRequest object. :param request: JSON string representing searchFeaturesRequest :return: JSON string representing searchFeatureResponse """ |
return self.runSearchRequest(
request, protocol.SearchFeaturesRequest,
protocol.SearchFeaturesResponse,
self.featuresGenerator) |
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def runSearchContinuousSets(self, request):
""" Returns a SearchContinuousSetsResponse for the specified SearchContinuousSetsRequest object. """ |
return self.runSearchRequest(
request, protocol.SearchContinuousSetsRequest,
protocol.SearchContinuousSetsResponse,
self.continuousSetsGenerator) |
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def runSearchContinuous(self, request):
""" Returns a SearchContinuousResponse for the specified SearchContinuousRequest object. :param request: JSON string representing searchContinuousRequest :return: JSON string representing searchContinuousResponse """ |
return self.runSearchRequest(
request, protocol.SearchContinuousRequest,
protocol.SearchContinuousResponse,
self.continuousGenerator) |
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def runSearchRnaQuantificationSets(self, request):
""" Returns a SearchRnaQuantificationSetsResponse for the specified SearchRnaQuantificationSetsRequest object. """ |
return self.runSearchRequest(
request, protocol.SearchRnaQuantificationSetsRequest,
protocol.SearchRnaQuantificationSetsResponse,
self.rnaQuantificationSetsGenerator) |
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def runSearchRnaQuantifications(self, request):
""" Returns a SearchRnaQuantificationResponse for the specified SearchRnaQuantificationRequest object. """ |
return self.runSearchRequest(
request, protocol.SearchRnaQuantificationsRequest,
protocol.SearchRnaQuantificationsResponse,
self.rnaQuantificationsGenerator) |
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def runSearchExpressionLevels(self, request):
""" Returns a SearchExpressionLevelResponse for the specified SearchExpressionLevelRequest object. """ |
return self.runSearchRequest(
request, protocol.SearchExpressionLevelsRequest,
protocol.SearchExpressionLevelsResponse,
self.expressionLevelsGenerator) |
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def populateFromRow(self, dataset):
""" Populates the instance variables of this Dataset from the specified database row. """ |
self._description = dataset.description
self.setAttributesJson(dataset.attributes) |
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def addVariantSet(self, variantSet):
""" Adds the specified variantSet to this dataset. """ |
id_ = variantSet.getId()
self._variantSetIdMap[id_] = variantSet
self._variantSetNameMap[variantSet.getLocalId()] = variantSet
self._variantSetIds.append(id_) |
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def addBiosample(self, biosample):
""" Adds the specified biosample to this dataset. """ |
id_ = biosample.getId()
self._biosampleIdMap[id_] = biosample
self._biosampleIds.append(id_)
self._biosampleNameMap[biosample.getName()] = biosample |
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def addIndividual(self, individual):
""" Adds the specified individual to this dataset. """ |
id_ = individual.getId()
self._individualIdMap[id_] = individual
self._individualIds.append(id_)
self._individualNameMap[individual.getName()] = individual |
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def addFeatureSet(self, featureSet):
""" Adds the specified featureSet to this dataset. """ |
id_ = featureSet.getId()
self._featureSetIdMap[id_] = featureSet
self._featureSetIds.append(id_)
name = featureSet.getLocalId()
self._featureSetNameMap[name] = featureSet |
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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()
self._continuousSetNameMap[name] = continuousSet |
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def addReadGroupSet(self, readGroupSet):
""" Adds the specified readGroupSet to this dataset. """ |
id_ = readGroupSet.getId()
self._readGroupSetIdMap[id_] = readGroupSet
self._readGroupSetNameMap[readGroupSet.getLocalId()] = readGroupSet
self._readGroupSetIds.append(id_) |
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def addRnaQuantificationSet(self, rnaQuantSet):
""" Adds the specified rnaQuantification set to this dataset. """ |
id_ = rnaQuantSet.getId()
self._rnaQuantificationSetIdMap[id_] = rnaQuantSet
self._rnaQuantificationSetIds.append(id_)
name = rnaQuantSet.getLocalId()
self._rnaQuantificationSetNameMap[name] = rnaQuantSet |
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def getVariantSet(self, id_):
""" Returns the VariantSet with the specified name, or raises a VariantSetNotFoundException otherwise. """ |
if id_ not in self._variantSetIdMap:
raise exceptions.VariantSetNotFoundException(id_)
return self._variantSetIdMap[id_] |
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def getVariantSetByName(self, name):
""" Returns a VariantSet with the specified name, or raises a VariantSetNameNotFoundException if it does not exist. """ |
if name not in self._variantSetNameMap:
raise exceptions.VariantSetNameNotFoundException(name)
return self._variantSetNameMap[name] |
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def addPhenotypeAssociationSet(self, phenotypeAssociationSet):
""" Adds the specified g2p association set to this backend. """ |
id_ = phenotypeAssociationSet.getId()
self._phenotypeAssociationSetIdMap[id_] = phenotypeAssociationSet
self._phenotypeAssociationSetNameMap[
phenotypeAssociationSet.getLocalId()] = phenotypeAssociationSet
self._phenotypeAssociationSetIds.append(id_) |
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def getFeatureSet(self, id_):
""" Returns the FeatureSet with the specified id, or raises a FeatureSetNotFoundException otherwise. """ |
if id_ not in self._featureSetIdMap:
raise exceptions.FeatureSetNotFoundException(id_)
return self._featureSetIdMap[id_] |
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def getFeatureSetByName(self, name):
""" Returns the FeatureSet with the specified name, or raises an exception otherwise. """ |
if name not in self._featureSetNameMap:
raise exceptions.FeatureSetNameNotFoundException(name)
return self._featureSetNameMap[name] |
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def getContinuousSet(self, id_):
""" Returns the ContinuousSet with the specified id, or raises a ContinuousSetNotFoundException otherwise. """ |
if id_ not in self._continuousSetIdMap:
raise exceptions.ContinuousSetNotFoundException(id_)
return self._continuousSetIdMap[id_] |
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def getContinuousSetByName(self, name):
""" Returns the ContinuousSet with the specified name, or raises an exception otherwise. """ |
if name not in self._continuousSetNameMap:
raise exceptions.ContinuousSetNameNotFoundException(name)
return self._continuousSetNameMap[name] |
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def getBiosampleByName(self, name):
""" Returns a Biosample with the specified name, or raises a BiosampleNameNotFoundException if it does not exist. """ |
if name not in self._biosampleNameMap:
raise exceptions.BiosampleNameNotFoundException(name)
return self._biosampleNameMap[name] |
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def getBiosample(self, id_):
""" Returns the Biosample with the specified id, or raises a BiosampleNotFoundException otherwise. """ |
if id_ not in self._biosampleIdMap:
raise exceptions.BiosampleNotFoundException(id_)
return self._biosampleIdMap[id_] |
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def getIndividualByName(self, name):
""" Returns an individual with the specified name, or raises a IndividualNameNotFoundException if it does not exist. """ |
if name not in self._individualNameMap:
raise exceptions.IndividualNameNotFoundException(name)
return self._individualNameMap[name] |
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def getIndividual(self, id_):
""" Returns the Individual with the specified id, or raises a IndividualNotFoundException otherwise. """ |
if id_ not in self._individualIdMap:
raise exceptions.IndividualNotFoundException(id_)
return self._individualIdMap[id_] |
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def getReadGroupSetByName(self, name):
""" Returns a ReadGroupSet with the specified name, or raises a ReadGroupSetNameNotFoundException if it does not exist. """ |
if name not in self._readGroupSetNameMap:
raise exceptions.ReadGroupSetNameNotFoundException(name)
return self._readGroupSetNameMap[name] |
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def getReadGroupSet(self, id_):
""" Returns the ReadGroupSet with the specified name, or raises a ReadGroupSetNotFoundException otherwise. """ |
if id_ not in self._readGroupSetIdMap:
raise exceptions.ReadGroupNotFoundException(id_)
return self._readGroupSetIdMap[id_] |
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def getRnaQuantificationSetByName(self, name):
""" Returns the RnaQuantification set with the specified name, or raises an exception otherwise. """ |
if name not in self._rnaQuantificationSetNameMap:
raise exceptions.RnaQuantificationSetNameNotFoundException(name)
return self._rnaQuantificationSetNameMap[name] |
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def getRnaQuantificationSet(self, id_):
""" Returns the RnaQuantification set with the specified name, or raises a RnaQuantificationSetNotFoundException otherwise. """ |
if id_ not in self._rnaQuantificationSetIdMap:
raise exceptions.RnaQuantificationSetNotFoundException(id_)
return self._rnaQuantificationSetIdMap[id_] |
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def addReadGroup(self, readGroup):
""" Adds the specified ReadGroup to this ReadGroupSet. """ |
id_ = readGroup.getId()
self._readGroupIdMap[id_] = readGroup
self._readGroupIds.append(id_) |
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def getReadGroup(self, id_):
""" Returns the ReadGroup with the specified id if it exists in this ReadGroupSet, or raises a ReadGroupNotFoundException otherwise. """ |
if id_ not in self._readGroupIdMap:
raise exceptions.ReadGroupNotFoundException(id_)
return self._readGroupIdMap[id_] |
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def toProtocolElement(self):
""" Returns the GA4GH protocol representation of this ReadGroupSet. """ |
readGroupSet = protocol.ReadGroupSet()
readGroupSet.id = self.getId()
readGroupSet.read_groups.extend(
[readGroup.toProtocolElement()
for readGroup in self.getReadGroups()]
)
readGroupSet.name = self.getLocalId()
readGroupSet.dataset_id = self.getParentContainer().getId()
readGroupSet.stats.CopyFrom(self.getStats())
self.serializeAttributes(readGroupSet)
return readGroupSet |
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def getReadAlignmentId(self, gaAlignment):
""" Returns a string ID suitable for use in the specified GA ReadAlignment object in this ReadGroupSet. """ |
compoundId = datamodel.ReadAlignmentCompoundId(
self.getCompoundId(), gaAlignment.fragment_name)
return str(compoundId) |
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def getStats(self):
""" Returns the GA4GH protocol representation of this read group set's ReadStats. """ |
stats = protocol.ReadStats()
stats.aligned_read_count = self._numAlignedReads
stats.unaligned_read_count = self._numUnalignedReads
return stats |
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def populateFromRow(self, readGroupSetRecord):
""" Populates the instance variables of this ReadGroupSet from the specified database row. """ |
self._dataUrl = readGroupSetRecord.dataurl
self._indexFile = readGroupSetRecord.indexfile
self._programs = []
for jsonDict in json.loads(readGroupSetRecord.programs):
program = protocol.fromJson(json.dumps(jsonDict),
protocol.Program)
self._programs.append(program)
stats = protocol.fromJson(readGroupSetRecord.stats, protocol.ReadStats)
self._numAlignedReads = stats.aligned_read_count
self._numUnalignedReads = stats.unaligned_read_count |
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def populateFromFile(self, dataUrl, indexFile=None):
""" Populates the instance variables of this ReadGroupSet from the specified dataUrl and indexFile. If indexFile is not specified guess usual form. """ |
self._dataUrl = dataUrl
self._indexFile = indexFile
if indexFile is None:
self._indexFile = dataUrl + ".bai"
samFile = self.getFileHandle(self._dataUrl)
self._setHeaderFields(samFile)
if 'RG' not in samFile.header or len(samFile.header['RG']) == 0:
readGroup = HtslibReadGroup(self, self.defaultReadGroupName)
self.addReadGroup(readGroup)
else:
for readGroupHeader in samFile.header['RG']:
readGroup = HtslibReadGroup(self, readGroupHeader['ID'])
readGroup.populateFromHeader(readGroupHeader)
self.addReadGroup(readGroup)
self._bamHeaderReferenceSetName = None
for referenceInfo in samFile.header['SQ']:
if 'AS' not in referenceInfo:
infoDict = parseMalformedBamHeader(referenceInfo)
else:
infoDict = referenceInfo
name = infoDict.get('AS', references.DEFAULT_REFERENCESET_NAME)
if self._bamHeaderReferenceSetName is None:
self._bamHeaderReferenceSetName = name
elif self._bamHeaderReferenceSetName != name:
raise exceptions.MultipleReferenceSetsInReadGroupSet(
self._dataUrl, name, self._bamFileReferenceName)
self._numAlignedReads = samFile.mapped
self._numUnalignedReads = samFile.unmapped |
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def toProtocolElement(self):
""" Returns the GA4GH protocol representation of this ReadGroup. """ |
# TODO this is very incomplete, but we don't have the
# implementation to fill out the rest of the fields currently
readGroup = protocol.ReadGroup()
readGroup.id = self.getId()
readGroup.created = self._creationTime
readGroup.updated = self._updateTime
dataset = self.getParentContainer().getParentContainer()
readGroup.dataset_id = dataset.getId()
readGroup.name = self.getLocalId()
readGroup.predicted_insert_size = pb.int(self.getPredictedInsertSize())
referenceSet = self._parentContainer.getReferenceSet()
readGroup.sample_name = pb.string(self.getSampleName())
readGroup.biosample_id = pb.string(self.getBiosampleId())
if referenceSet is not None:
readGroup.reference_set_id = referenceSet.getId()
readGroup.stats.CopyFrom(self.getStats())
readGroup.programs.extend(self.getPrograms())
readGroup.description = pb.string(self.getDescription())
readGroup.experiment.CopyFrom(self.getExperiment())
self.serializeAttributes(readGroup)
return readGroup |
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def getStats(self):
""" Returns the GA4GH protocol representation of this read group's ReadStats. """ |
stats = protocol.ReadStats()
stats.aligned_read_count = self.getNumAlignedReads()
stats.unaligned_read_count = self.getNumUnalignedReads()
# TODO base_count requires iterating through all reads
return stats |
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def getExperiment(self):
""" Returns the GA4GH protocol representation of this read group's Experiment. """ |
experiment = protocol.Experiment()
experiment.id = self.getExperimentId()
experiment.instrument_model = pb.string(self.getInstrumentModel())
experiment.sequencing_center = pb.string(self.getSequencingCenter())
experiment.description = pb.string(self.getExperimentDescription())
experiment.library = pb.string(self.getLibrary())
experiment.platform_unit = pb.string(self.getPlatformUnit())
experiment.message_create_time = self._iso8601
experiment.message_update_time = self._iso8601
experiment.run_time = pb.string(self.getRunTime())
return experiment |
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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._predictedInsertSize = int(readGroupHeader['PI'])
self._instrumentModel = readGroupHeader.get('PL', None)
self._sequencingCenter = readGroupHeader.get('CN', None)
self._experimentDescription = readGroupHeader.get('DS', None)
self._library = readGroupHeader.get('LB', None)
self._platformUnit = readGroupHeader.get('PU', None)
self._runTime = readGroupHeader.get('DT', None) |
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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._predictedInsertSize = readGroupRecord.predictedinsertsize
stats = protocol.fromJson(readGroupRecord.stats, protocol.ReadStats)
self._numAlignedReads = stats.aligned_read_count
self._numUnalignedReads = stats.unaligned_read_count
experiment = protocol.fromJson(
readGroupRecord.experiment, protocol.Experiment)
self._instrumentModel = experiment.instrument_model
self._sequencingCenter = experiment.sequencing_center
self._experimentDescription = experiment.description
self._library = experiment.library
self._platformUnit = experiment.platform_unit
self._runTime = experiment.run_time |
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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.normpath(filePath))[1]
# We need to handle things like .fa.gz, so we can't use
# os.path.splitext
ret = fileName.split(".")[0]
assert ret != ""
return ret |
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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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def _updateRepo(self, func, *args, **kwargs):
""" Runs the specified function that updates the repo with the specified arguments. This method ensures that all updates are transactional, so that if any part of the update fails no changes are made to the repo. """ |
# TODO how do we make this properly transactional?
self._repo.open(datarepo.MODE_WRITE)
try:
func(*args, **kwargs)
self._repo.commit()
finally:
self._repo.close() |
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def addOntology(self):
""" Adds a new Ontology to this repo. """ |
self._openRepo()
name = self._args.name
filePath = self._getFilePath(self._args.filePath,
self._args.relativePath)
if name is None:
name = getNameFromPath(filePath)
ontology = ontologies.Ontology(name)
ontology.populateFromFile(filePath)
self._updateRepo(self._repo.insertOntology, ontology) |
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def addDataset(self):
""" Adds a new dataset into this repo. """ |
self._openRepo()
dataset = datasets.Dataset(self._args.datasetName)
dataset.setDescription(self._args.description)
dataset.setAttributes(json.loads(self._args.attributes))
self._updateRepo(self._repo.insertDataset, dataset) |
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def addReferenceSet(self):
""" Adds a new reference set into this repo. """ |
self._openRepo()
name = self._args.name
filePath = self._getFilePath(self._args.filePath,
self._args.relativePath)
if name is None:
name = getNameFromPath(self._args.filePath)
referenceSet = references.HtslibReferenceSet(name)
referenceSet.populateFromFile(filePath)
referenceSet.setDescription(self._args.description)
if self._args.species is not None:
referenceSet.setSpeciesFromJson(self._args.species)
referenceSet.setIsDerived(self._args.isDerived)
referenceSet.setAssemblyId(self._args.assemblyId)
referenceSet.setAttributes(json.loads(self._args.attributes))
sourceAccessions = []
if self._args.sourceAccessions is not None:
sourceAccessions = self._args.sourceAccessions.split(",")
referenceSet.setSourceAccessions(sourceAccessions)
referenceSet.setSourceUri(self._args.sourceUri)
self._updateRepo(self._repo.insertReferenceSet, referenceSet) |
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def addReadGroupSet(self):
""" Adds a new ReadGroupSet into this repo. """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
dataUrl = self._args.dataFile
indexFile = self._args.indexFile
parsed = urlparse.urlparse(dataUrl)
# TODO, add https support and others when they have been
# tested.
if parsed.scheme in ['http', 'ftp']:
if indexFile is None:
raise exceptions.MissingIndexException(dataUrl)
else:
if indexFile is None:
indexFile = dataUrl + ".bai"
dataUrl = self._getFilePath(self._args.dataFile,
self._args.relativePath)
indexFile = self._getFilePath(indexFile, self._args.relativePath)
name = self._args.name
if self._args.name is None:
name = getNameFromPath(dataUrl)
readGroupSet = reads.HtslibReadGroupSet(dataset, name)
readGroupSet.populateFromFile(dataUrl, indexFile)
referenceSetName = self._args.referenceSetName
if referenceSetName is None:
# Try to find a reference set name from the BAM header.
referenceSetName = readGroupSet.getBamHeaderReferenceSetName()
referenceSet = self._repo.getReferenceSetByName(referenceSetName)
readGroupSet.setReferenceSet(referenceSet)
readGroupSet.setAttributes(json.loads(self._args.attributes))
self._updateRepo(self._repo.insertReadGroupSet, readGroupSet) |
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def addPhenotypeAssociationSet(self):
""" Adds a new phenotype association set to this repo. """ |
self._openRepo()
name = self._args.name
if name is None:
name = getNameFromPath(self._args.dirPath)
dataset = self._repo.getDatasetByName(self._args.datasetName)
phenotypeAssociationSet = \
genotype_phenotype.RdfPhenotypeAssociationSet(
dataset, name, self._args.dirPath)
phenotypeAssociationSet.setAttributes(
json.loads(self._args.attributes))
self._updateRepo(
self._repo.insertPhenotypeAssociationSet,
phenotypeAssociationSet) |
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def removePhenotypeAssociationSet(self):
""" Removes a phenotype association set from the repo """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSetByName(
self._args.name)
def func():
self._updateRepo(
self._repo.removePhenotypeAssociationSet,
phenotypeAssociationSet)
self._confirmDelete(
"PhenotypeAssociationSet",
phenotypeAssociationSet.getLocalId(),
func) |
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def removeReferenceSet(self):
""" Removes a referenceSet from the repo. """ |
self._openRepo()
referenceSet = self._repo.getReferenceSetByName(
self._args.referenceSetName)
def func():
self._updateRepo(self._repo.removeReferenceSet, referenceSet)
self._confirmDelete("ReferenceSet", referenceSet.getLocalId(), func) |
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def removeReadGroupSet(self):
""" Removes a readGroupSet from the repo. """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
readGroupSet = dataset.getReadGroupSetByName(
self._args.readGroupSetName)
def func():
self._updateRepo(self._repo.removeReadGroupSet, readGroupSet)
self._confirmDelete("ReadGroupSet", readGroupSet.getLocalId(), func) |
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def removeVariantSet(self):
""" Removes a variantSet from the repo. """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
variantSet = dataset.getVariantSetByName(self._args.variantSetName)
def func():
self._updateRepo(self._repo.removeVariantSet, variantSet)
self._confirmDelete("VariantSet", variantSet.getLocalId(), func) |
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def removeDataset(self):
""" Removes a dataset from the repo. """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
def func():
self._updateRepo(self._repo.removeDataset, dataset)
self._confirmDelete("Dataset", dataset.getLocalId(), func) |
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def addFeatureSet(self):
""" Adds a new feature set into this repo """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
filePath = self._getFilePath(self._args.filePath,
self._args.relativePath)
name = getNameFromPath(self._args.filePath)
featureSet = sequence_annotations.Gff3DbFeatureSet(
dataset, name)
referenceSetName = self._args.referenceSetName
if referenceSetName is None:
raise exceptions.RepoManagerException(
"A reference set name must be provided")
referenceSet = self._repo.getReferenceSetByName(referenceSetName)
featureSet.setReferenceSet(referenceSet)
ontologyName = self._args.ontologyName
if ontologyName is None:
raise exceptions.RepoManagerException(
"A sequence ontology name must be provided")
ontology = self._repo.getOntologyByName(ontologyName)
self._checkSequenceOntology(ontology)
featureSet.setOntology(ontology)
featureSet.populateFromFile(filePath)
featureSet.setAttributes(json.loads(self._args.attributes))
self._updateRepo(self._repo.insertFeatureSet, featureSet) |
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def removeFeatureSet(self):
""" Removes a feature set from this repo """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
featureSet = dataset.getFeatureSetByName(self._args.featureSetName)
def func():
self._updateRepo(self._repo.removeFeatureSet, featureSet)
self._confirmDelete("FeatureSet", featureSet.getLocalId(), func) |
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def addContinuousSet(self):
""" Adds a new continuous set into this repo """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
filePath = self._getFilePath(self._args.filePath,
self._args.relativePath)
name = getNameFromPath(self._args.filePath)
continuousSet = continuous.FileContinuousSet(dataset, name)
referenceSetName = self._args.referenceSetName
if referenceSetName is None:
raise exceptions.RepoManagerException(
"A reference set name must be provided")
referenceSet = self._repo.getReferenceSetByName(referenceSetName)
continuousSet.setReferenceSet(referenceSet)
continuousSet.populateFromFile(filePath)
self._updateRepo(self._repo.insertContinuousSet, continuousSet) |
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Description:
def removeContinuousSet(self):
""" Removes a continuous set from this repo """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
continuousSet = dataset.getContinuousSetByName(
self._args.continuousSetName)
def func():
self._updateRepo(self._repo.removeContinuousSet, continuousSet)
self._confirmDelete("ContinuousSet", continuousSet.getLocalId(), func) |
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Description:
def addBiosample(self):
""" Adds a new biosample into this repo """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
biosample = bio_metadata.Biosample(
dataset, self._args.biosampleName)
biosample.populateFromJson(self._args.biosample)
self._updateRepo(self._repo.insertBiosample, biosample) |
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Description:
def removeBiosample(self):
""" Removes a biosample from this repo """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
biosample = dataset.getBiosampleByName(self._args.biosampleName)
def func():
self._updateRepo(self._repo.removeBiosample, biosample)
self._confirmDelete("Biosample", biosample.getLocalId(), func) |
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Description:
def addIndividual(self):
""" Adds a new individual into this repo """ |
self._openRepo()
dataset = self._repo.getDatasetByName(self._args.datasetName)
individual = bio_metadata.Individual(
dataset, self._args.individualName)
individual.populateFromJson(self._args.individual)
self._updateRepo(self._repo.insertIndividual, individual) |
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