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stringlengths 52
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def generateVariantAnnotation(self, variant):
"""
Generate a random variant annotation based on a given variant.
This generator should be seeded with a value that is unique to the
variant so that the same annotation will always be produced regardless
of the order it is generated in.
"""
# To make this reproducible, make a seed based on this
# specific variant.
seed = self._randomSeed + variant.start + variant.end
randomNumberGenerator = random.Random()
randomNumberGenerator.seed(seed)
ann = protocol.VariantAnnotation()
ann.variant_annotation_set_id = str(self.getCompoundId())
ann.variant_id = variant.id
ann.created = datetime.datetime.now().isoformat() + "Z"
# make a transcript effect for each alternate base element
# multiplied by a random integer (1,5)
for base in variant.alternate_bases:
ann.transcript_effects.add().CopyFrom(
self.generateTranscriptEffect(
variant, ann, base, randomNumberGenerator))
ann.id = self.getVariantAnnotationId(variant, ann)
return ann | Generate a random variant annotation based on a given variant.
This generator should be seeded with a value that is unique to the
variant so that the same annotation will always be produced regardless
of the order it is generated in. | entailment |
def populateFromRow(self, annotationSetRecord):
"""
Populates this VariantAnnotationSet from the specified DB row.
"""
self._annotationType = annotationSetRecord.annotationtype
self._analysis = protocol.fromJson(
annotationSetRecord.analysis, protocol.Analysis)
self._creationTime = annotationSetRecord.created
self._updatedTime = annotationSetRecord.updated
self.setAttributesJson(annotationSetRecord.attributes) | Populates this VariantAnnotationSet from the specified DB row. | entailment |
def _getAnnotationAnalysis(self, varFile):
"""
Assembles metadata within the VCF header into a GA4GH Analysis object.
:return: protocol.Analysis
"""
header = varFile.header
analysis = protocol.Analysis()
formats = header.formats.items()
infos = header.info.items()
filters = header.filters.items()
for prefix, content in [("FORMAT", formats), ("INFO", infos),
("FILTER", filters)]:
for contentKey, value in content:
key = "{0}.{1}".format(prefix, value.name)
if key not in analysis.attributes.attr:
analysis.attributes.attr[key].Clear()
if value.description is not None:
analysis.attributes.attr[
key].values.add().string_value = value.description
analysis.created = self._creationTime
analysis.updated = self._updatedTime
for r in header.records:
# Don't add a key to info if there's nothing in the value
if r.value is not None:
if r.key not in analysis.attributes.attr:
analysis.attributes.attr[r.key].Clear()
analysis.attributes.attr[r.key] \
.values.add().string_value = str(r.value)
if r.key == "created" or r.key == "fileDate":
# TODO handle more date formats
try:
if '-' in r.value:
fmtStr = "%Y-%m-%d"
else:
fmtStr = "%Y%m%d"
analysis.created = datetime.datetime.strptime(
r.value, fmtStr).isoformat() + "Z"
except ValueError:
# is there a logger we should tell?
# print("INFO: Could not parse variant annotation time")
pass # analysis.create_date_time remains datetime.now()
if r.key == "software":
analysis.software.append(r.value)
if r.key == "name":
analysis.name = r.value
if r.key == "description":
analysis.description = r.value
analysis.id = str(datamodel.VariantAnnotationSetAnalysisCompoundId(
self._compoundId, "analysis"))
return analysis | Assembles metadata within the VCF header into a GA4GH Analysis object.
:return: protocol.Analysis | entailment |
def getVariantAnnotations(self, referenceName, startPosition, endPosition):
"""
Generator for iterating through variant annotations in this
variant annotation set.
:param referenceName:
:param startPosition:
:param endPosition:
:return: generator of protocol.VariantAnnotation
"""
variantIter = self._variantSet.getPysamVariants(
referenceName, startPosition, endPosition)
for record in variantIter:
yield self.convertVariantAnnotation(record) | Generator for iterating through variant annotations in this
variant annotation set.
:param referenceName:
:param startPosition:
:param endPosition:
:return: generator of protocol.VariantAnnotation | entailment |
def convertLocation(self, pos):
"""
Accepts a position string (start/length) and returns
a GA4GH AlleleLocation with populated fields.
:param pos:
:return: protocol.AlleleLocation
"""
if isUnspecified(pos):
return None
coordLen = pos.split('/')
if len(coordLen) > 1:
allLoc = self._createGaAlleleLocation()
allLoc.start = int(coordLen[0]) - 1
return allLoc
return None | Accepts a position string (start/length) and returns
a GA4GH AlleleLocation with populated fields.
:param pos:
:return: protocol.AlleleLocation | entailment |
def convertLocationHgvsC(self, hgvsc):
"""
Accepts an annotation in HGVS notation and returns
an AlleleLocation with populated fields.
:param hgvsc:
:return:
"""
if isUnspecified(hgvsc):
return None
match = re.match(".*c.(\d+)(\D+)>(\D+)", hgvsc)
if match:
pos = int(match.group(1))
if pos > 0:
allLoc = self._createGaAlleleLocation()
allLoc.start = pos - 1
allLoc.reference_sequence = match.group(2)
allLoc.alternate_sequence = match.group(3)
return allLoc
return None | Accepts an annotation in HGVS notation and returns
an AlleleLocation with populated fields.
:param hgvsc:
:return: | entailment |
def convertLocationHgvsP(self, hgvsp):
"""
Accepts an annotation in HGVS notation and returns
an AlleleLocation with populated fields.
:param hgvsp:
:return: protocol.AlleleLocation
"""
if isUnspecified(hgvsp):
return None
match = re.match(".*p.(\D+)(\d+)(\D+)", hgvsp, flags=re.UNICODE)
if match is not None:
allLoc = self._createGaAlleleLocation()
allLoc.reference_sequence = match.group(1)
allLoc.start = int(match.group(2)) - 1
allLoc.alternate_sequence = match.group(3)
return allLoc
return None | Accepts an annotation in HGVS notation and returns
an AlleleLocation with populated fields.
:param hgvsp:
:return: protocol.AlleleLocation | entailment |
def addLocations(self, effect, protPos, cdnaPos):
"""
Adds locations to a GA4GH transcript effect object
by parsing HGVS annotation fields in concert with
and supplied position values.
:param effect: protocol.TranscriptEffect
:param protPos: String representing protein position from VCF
:param cdnaPos: String representing coding DNA location
:return: effect protocol.TranscriptEffect
"""
self.addCDSLocation(effect, cdnaPos)
self.addCDNALocation(effect, cdnaPos)
self.addProteinLocation(effect, protPos)
return effect | Adds locations to a GA4GH transcript effect object
by parsing HGVS annotation fields in concert with
and supplied position values.
:param effect: protocol.TranscriptEffect
:param protPos: String representing protein position from VCF
:param cdnaPos: String representing coding DNA location
:return: effect protocol.TranscriptEffect | entailment |
def convertTranscriptEffect(self, annStr, hgvsG):
"""
Takes the ANN string of a SnpEff generated VCF, splits it
and returns a populated GA4GH transcript effect object.
:param annStr: String
:param hgvsG: String
:return: effect protocol.TranscriptEffect()
"""
effect = self._createGaTranscriptEffect()
effect.hgvs_annotation.CopyFrom(protocol.HGVSAnnotation())
annDict = dict()
if self._annotationType == ANNOTATIONS_SNPEFF:
annDict = dict(zip(self. SNPEFF_FIELDS, annStr.split("|")))
elif self._annotationType == ANNOTATIONS_VEP_V82:
annDict = dict(zip(self.VEP_FIELDS, annStr.split("|")))
else:
annDict = dict(zip(self.CSQ_FIELDS, annStr.split("|")))
annDict["hgvs_annotation.genomic"] = hgvsG if hgvsG else u''
for key, val in annDict.items():
try:
protocol.deepSetAttr(effect, key, val)
except AttributeError:
if val and key not in self.EXCLUDED_FIELDS:
protocol.setAttribute(
effect.attributes.attr[key].values, val)
effect.effects.extend(self.convertSeqOntology(annDict.get('effects')))
self.addLocations(
effect, annDict.get('protPos'), annDict.get('cdnaPos'))
effect.id = self.getTranscriptEffectId(effect)
return effect | Takes the ANN string of a SnpEff generated VCF, splits it
and returns a populated GA4GH transcript effect object.
:param annStr: String
:param hgvsG: String
:return: effect protocol.TranscriptEffect() | entailment |
def convertSeqOntology(self, seqOntStr):
"""
Splits a string of sequence ontology effects and creates
an ontology term record for each, which are built into
an array of return soTerms.
:param seqOntStr:
:return: [protocol.OntologyTerm]
"""
return [
self._ontology.getGaTermByName(soName)
for soName in seqOntStr.split('&')] | Splits a string of sequence ontology effects and creates
an ontology term record for each, which are built into
an array of return soTerms.
:param seqOntStr:
:return: [protocol.OntologyTerm] | entailment |
def convertVariantAnnotation(self, record):
"""
Converts the specfied pysam variant record into a GA4GH variant
annotation object using the specified function to convert the
transcripts.
"""
variant = self._variantSet.convertVariant(record, [])
annotation = self._createGaVariantAnnotation()
annotation.variant_id = variant.id
gDots = record.info.get(b'HGVS.g')
# Convert annotations from INFO field into TranscriptEffect
transcriptEffects = []
annotations = record.info.get(b'ANN') or record.info.get(b'CSQ')
for i, ann in enumerate(annotations):
hgvsG = gDots[i % len(variant.alternate_bases)] if gDots else None
transcriptEffects.append(self.convertTranscriptEffect(ann, hgvsG))
annotation.transcript_effects.extend(transcriptEffects)
annotation.id = self.getVariantAnnotationId(variant, annotation)
return variant, annotation | Converts the specfied pysam variant record into a GA4GH variant
annotation object using the specified function to convert the
transcripts. | entailment |
def _attributeStr(self, name):
"""
Return name=value for a single attribute
"""
return "{}={}".format(
_encodeAttr(name),
",".join([_encodeAttr(v) for v in self.attributes[name]])) | Return name=value for a single attribute | entailment |
def _attributeStrs(self):
"""
Return name=value, semi-colon-separated string for attributes,
including url-style quoting
"""
return ";".join([self._attributeStr(name)
for name in self.attributes.iterkeys()]) | Return name=value, semi-colon-separated string for attributes,
including url-style quoting | entailment |
def featureName(self):
"""
ID attribute from GFF3 or None if record doesn't have it.
Called "Name" rather than "Id" within GA4GH, as there is
no guarantee of either uniqueness or existence.
"""
featId = self.attributes.get("ID")
if featId is not None:
featId = featId[0]
return featId | ID attribute from GFF3 or None if record doesn't have it.
Called "Name" rather than "Id" within GA4GH, as there is
no guarantee of either uniqueness or existence. | entailment |
def _linkFeature(self, feature):
"""
Link a feature with its parents.
"""
parentNames = feature.attributes.get("Parent")
if parentNames is None:
self.roots.add(feature)
else:
for parentName in parentNames:
self._linkToParent(feature, parentName) | Link a feature with its parents. | entailment |
def _linkToParent(self, feature, parentName):
"""
Link a feature with its children
"""
parentParts = self.byFeatureName.get(parentName)
if parentParts is None:
raise GFF3Exception(
"Parent feature does not exist: {}".format(parentName),
self.fileName)
# parent maybe disjoint
for parentPart in parentParts:
feature.parents.add(parentPart)
parentPart.children.add(feature) | Link a feature with its children | entailment |
def linkChildFeaturesToParents(self):
"""
finish loading the set, constructing the tree
"""
# features maybe disjoint
for featureParts in self.byFeatureName.itervalues():
for feature in featureParts:
self._linkFeature(feature) | finish loading the set, constructing the tree | entailment |
def _recSortKey(r):
"""
Sort order for Features, by genomic coordinate,
disambiguated by feature type (alphabetically).
"""
return r.seqname, r.start, -r.end, r.type | Sort order for Features, by genomic coordinate,
disambiguated by feature type (alphabetically). | entailment |
def _writeRec(self, fh, rec):
"""
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):
self._writeRec(fh, child) | Writes a single record to a file provided by the filehandle fh. | entailment |
def write(self, fh):
"""
Write set to a GFF3 format file.
:param file fh: file handle for file to write to
"""
fh.write(GFF3_HEADER+"\n")
for root in sorted(self.roots, key=self._recSortKey):
self._writeRec(fh, root) | Write set to a GFF3 format file.
:param file fh: file handle for file to write to | entailment |
def _open(self):
"""
open input file, optionally with decompression
"""
if self.fileName.endswith(".gz"):
return gzip.open(self.fileName)
elif self.fileName.endswith(".bz2"):
return bz2.BZ2File(self.fileName)
else:
return open(self.fileName) | open input file, optionally with decompression | entailment |
def _parseAttrVal(self, attrStr):
"""
Returns tuple of tuple of (attr, value), multiple are returned to
handle multi-value attributes.
"""
m = self.SPLIT_ATTR_RE.match(attrStr)
if m is None:
raise GFF3Exception(
"can't parse attribute/value: '" + attrStr +
"'", self.fileName, self.lineNumber)
name = urllib.unquote(m.group(1))
val = m.group(2)
# Split by comma to separate then unquote.
# Commas in values must be url encoded.
return name, [urllib.unquote(v) for v in val.split(',')] | Returns tuple of tuple of (attr, value), multiple are returned to
handle multi-value attributes. | entailment |
def _parseAttrs(self, attrsStr):
"""
Parse the attributes and values
"""
attributes = dict()
for attrStr in self.SPLIT_ATTR_COL_RE.split(attrsStr):
name, vals = self._parseAttrVal(attrStr)
if name in attributes:
raise GFF3Exception(
"duplicated attribute name: {}".format(name),
self.fileName, self.lineNumber)
attributes[name] = vals
return attributes | Parse the attributes and values | entailment |
def _parseRecord(self, gff3Set, line):
"""
Parse one record.
"""
row = line.split("\t")
if len(row) != self.GFF3_NUM_COLS:
raise GFF3Exception(
"Wrong number of columns, expected {}, got {}".format(
self.GFF3_NUM_COLS, len(row)),
self.fileName, self.lineNumber)
feature = Feature(
urllib.unquote(row[0]),
urllib.unquote(row[1]),
urllib.unquote(row[2]),
int(row[3]), int(row[4]),
row[5], row[6], row[7],
self._parseAttrs(row[8]))
gff3Set.add(feature) | Parse one record. | entailment |
def parse(self):
"""
Run the parse and return the resulting Gff3Set object.
"""
fh = self._open()
try:
gff3Set = Gff3Set(self.fileName)
for line in fh:
self.lineNumber += 1
self._parseLine(gff3Set, line[0:-1])
finally:
fh.close()
gff3Set.linkChildFeaturesToParents()
return gff3Set | Run the parse and return the resulting Gff3Set object. | entailment |
def addDataset(self, dataset):
"""
Adds the specified dataset to this data repository.
"""
id_ = dataset.getId()
self._datasetIdMap[id_] = dataset
self._datasetNameMap[dataset.getLocalId()] = dataset
self._datasetIds.append(id_) | Adds the specified dataset to this data repository. | entailment |
def addReferenceSet(self, referenceSet):
"""
Adds the specified reference set to this data repository.
"""
id_ = referenceSet.getId()
self._referenceSetIdMap[id_] = referenceSet
self._referenceSetNameMap[referenceSet.getLocalId()] = referenceSet
self._referenceSetIds.append(id_) | Adds the specified reference set to this data repository. | entailment |
def addOntology(self, ontology):
"""
Add an ontology map to this data repository.
"""
self._ontologyNameMap[ontology.getName()] = ontology
self._ontologyIdMap[ontology.getId()] = ontology
self._ontologyIds.append(ontology.getId()) | Add an ontology map to this data repository. | entailment |
def getPeer(self, url):
"""
Select the first peer in the datarepo with the given url simulating
the behavior of selecting by URL. This is only used during testing.
"""
peers = filter(lambda x: x.getUrl() == url, self.getPeers())
if len(peers) == 0:
raise exceptions.PeerNotFoundException(url)
return peers[0] | Select the first peer in the datarepo with the given url simulating
the behavior of selecting by URL. This is only used during testing. | entailment |
def getDataset(self, id_):
"""
Returns a dataset with the specified ID, or raises a
DatasetNotFoundException if it does not exist.
"""
if id_ not in self._datasetIdMap:
raise exceptions.DatasetNotFoundException(id_)
return self._datasetIdMap[id_] | Returns a dataset with the specified ID, or raises a
DatasetNotFoundException if it does not exist. | entailment |
def getDatasetByName(self, name):
"""
Returns the dataset with the specified name.
"""
if name not in self._datasetNameMap:
raise exceptions.DatasetNameNotFoundException(name)
return self._datasetNameMap[name] | Returns the dataset with the specified name. | entailment |
def getOntology(self, id_):
"""
Returns the ontology with the specified ID.
"""
if id_ not in self._ontologyIdMap:
raise exceptions.OntologyNotFoundException(id_)
return self._ontologyIdMap[id_] | Returns the ontology with the specified ID. | entailment |
def getOntologyByName(self, name):
"""
Returns an ontology by name
"""
if name not in self._ontologyNameMap:
raise exceptions.OntologyNameNotFoundException(name)
return self._ontologyNameMap[name] | Returns an ontology by name | entailment |
def getReferenceSet(self, id_):
"""
Retuns the ReferenceSet with the specified ID, or raises a
ReferenceSetNotFoundException if it does not exist.
"""
if id_ not in self._referenceSetIdMap:
raise exceptions.ReferenceSetNotFoundException(id_)
return self._referenceSetIdMap[id_] | Retuns the ReferenceSet with the specified ID, or raises a
ReferenceSetNotFoundException if it does not exist. | entailment |
def getReferenceSetByName(self, name):
"""
Returns the reference set with the specified name.
"""
if name not in self._referenceSetNameMap:
raise exceptions.ReferenceSetNameNotFoundException(name)
return self._referenceSetNameMap[name] | Returns the reference set with the specified name. | entailment |
def getReadGroupSet(self, id_):
"""
Returns the readgroup set with the specified ID.
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataset(compoundId.dataset_id)
return dataset.getReadGroupSet(id_) | Returns the readgroup set with the specified ID. | entailment |
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_) | Returns the readgroup set with the specified ID. | entailment |
def printSummary(self):
"""
Prints a summary of this data repository to stdout.
"""
print("Ontologies:")
for ontology in self.getOntologys():
print(
"",
ontology.getOntologyPrefix(),
ontology.getName(),
ontology.getDataUrl(),
sep="\t")
print("ReferenceSets:")
for referenceSet in self.getReferenceSets():
print(
"", referenceSet.getLocalId(), referenceSet.getId(),
referenceSet.getDescription(), referenceSet.getDataUrl(),
sep="\t")
for reference in referenceSet.getReferences():
print(
"\t", reference.getLocalId(), reference.getId(),
sep="\t")
print("Datasets:")
for dataset in self.getDatasets():
print(
"", dataset.getLocalId(), dataset.getId(),
dataset.getDescription(), sep="\t")
print("\tReadGroupSets:")
for readGroupSet in dataset.getReadGroupSets():
print(
"\t", readGroupSet.getLocalId(),
readGroupSet.getReferenceSet().getLocalId(),
readGroupSet.getId(),
readGroupSet.getDataUrl(), sep="\t")
for readGroup in readGroupSet.getReadGroups():
print(
"\t\t", readGroup.getId(), readGroup.getLocalId(),
sep="\t")
print("\tVariantSets:")
for variantSet in dataset.getVariantSets():
print(
"\t", variantSet.getLocalId(),
variantSet.getReferenceSet().getLocalId(),
variantSet.getId(),
sep="\t")
if variantSet.getNumVariantAnnotationSets() > 0:
print("\t\tVariantAnnotationSets:")
for vas in variantSet.getVariantAnnotationSets():
print(
"\t\t", vas.getLocalId(),
vas.getAnnotationType(),
vas.getOntology().getName(), sep="\t")
print("\tFeatureSets:")
for featureSet in dataset.getFeatureSets():
print(
"\t", featureSet.getLocalId(),
featureSet.getReferenceSet().getLocalId(),
featureSet.getOntology().getName(),
featureSet.getId(),
sep="\t")
print("\tContinuousSets:")
for continuousSet in dataset.getContinuousSets():
print(
"\t", continuousSet.getLocalId(),
continuousSet.getReferenceSet().getLocalId(),
continuousSet.getId(),
sep="\t")
print("\tPhenotypeAssociationSets:")
for phenotypeAssociationSet in \
dataset.getPhenotypeAssociationSets():
print(
"\t", phenotypeAssociationSet.getLocalId(),
phenotypeAssociationSet.getParentContainer().getId(),
sep="\t")
# TODO - please improve this listing
print("\tRnaQuantificationSets:")
for rna_quantification_set in dataset.getRnaQuantificationSets():
print(
"\t", rna_quantification_set.getLocalId(),
rna_quantification_set.getId(), sep="\t")
for quant in rna_quantification_set.getRnaQuantifications():
print(
"\t\t", quant.getLocalId(),
quant._description,
",".join(quant._readGroupIds),
",".join(quant._featureSetIds), sep="\t") | Prints a summary of this data repository to stdout. | entailment |
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 | Return an iterator over all read groups in the data repo | entailment |
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 | Return an iterator over all features in the data repo | entailment |
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 | Return an iterator over all call sets in the data repo | entailment |
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():
yield vaSet | Return an iterator over all variant annotation sets
in the data repo | entailment |
def allRnaQuantifications(self):
"""
Return an iterator over all rna quantifications
"""
for dataset in self.getDatasets():
for rnaQuantificationSet in dataset.getRnaQuantificationSets():
for rnaQuantification in \
rnaQuantificationSet.getRnaQuantifications():
yield rnaQuantification | Return an iterator over all rna quantifications | entailment |
def allExpressionLevels(self):
"""
Return an iterator over all expression levels
"""
for dataset in self.getDatasets():
for rnaQuantificationSet in dataset.getRnaQuantificationSets():
for rnaQuantification in \
rnaQuantificationSet.getRnaQuantifications():
for expressionLevel in \
rnaQuantification.getExpressionLevels():
yield expressionLevel | Return an iterator over all expression levels | entailment |
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] | Finds a peer by URL and return the first peer record with that URL. | entailment |
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.url, record=p) for p in select] | Get the list of peers using an SQL offset and limit. Returns a list
of peer datamodel objects in a list. | entailment |
def tableToTsv(self, model):
"""
Takes a model class and attempts to create a table in TSV format
that can be imported into a spreadsheet program.
"""
first = True
for item in model.select():
if first:
header = "".join(
["{}\t".format(x) for x in model._meta.fields.keys()])
print(header)
first = False
row = "".join(
["{}\t".format(
getattr(item, key)) for key in model._meta.fields.keys()])
print(row) | Takes a model class and attempts to create a table in TSV format
that can be imported into a spreadsheet program. | entailment |
def clearAnnouncements(self):
"""
Flushes the announcement table.
"""
try:
q = models.Announcement.delete().where(
models.Announcement.id > 0)
q.execute()
except Exception as e:
raise exceptions.RepoManagerException(e) | Flushes the announcement table. | entailment |
def insertAnnouncement(self, announcement):
"""
Adds an announcement to the registry for later analysis.
"""
url = announcement.get('url', None)
try:
peers.Peer(url)
except:
raise exceptions.BadUrlException(url)
try:
# TODO get more details about the user agent
models.Announcement.create(
url=announcement.get('url'),
attributes=json.dumps(announcement.get('attributes', {})),
remote_addr=announcement.get('remote_addr', None),
user_agent=announcement.get('user_agent', None))
except Exception as e:
raise exceptions.RepoManagerException(e) | Adds an announcement to the registry for later analysis. | entailment |
def open(self, mode=MODE_READ):
"""
Opens this repo in the specified mode.
TODO: figure out the correct semantics of this and document
the intended future behaviour as well as the current
transitional behaviour.
"""
if mode not in [MODE_READ, MODE_WRITE]:
error = "Open mode must be '{}' or '{}'".format(
MODE_READ, MODE_WRITE)
raise ValueError(error)
self._openMode = mode
if mode == MODE_READ:
self.assertExists()
if mode == MODE_READ:
# This is part of the transitional behaviour where
# we load the whole DB into memory to get access to
# the data model.
self.load() | Opens this repo in the specified mode.
TODO: figure out the correct semantics of this and document
the intended future behaviour as well as the current
transitional behaviour. | entailment |
def verify(self):
"""
Verifies that the data in the repository is consistent.
"""
# TODO this should emit to a log that we can configure so we can
# have verbosity levels. We should provide a way to configure
# where we look at various chromosomes and so on. This will be
# an important debug tool for administrators.
for ontology in self.getOntologys():
print(
"Verifying Ontology", ontology.getName(),
"@", ontology.getDataUrl())
# TODO how do we verify this? Check some well-know SO terms?
for referenceSet in self.getReferenceSets():
print(
"Verifying ReferenceSet", referenceSet.getLocalId(),
"@", referenceSet.getDataUrl())
for reference in referenceSet.getReferences():
length = min(reference.getLength(), 1000)
bases = reference.getBases(0, length)
assert len(bases) == length
print(
"\tReading", length, "bases from",
reference.getLocalId())
for dataset in self.getDatasets():
print("Verifying Dataset", dataset.getLocalId())
for featureSet in dataset.getFeatureSets():
for referenceSet in self.getReferenceSets():
# TODO cycle through references?
reference = referenceSet.getReferences()[0]
print(
"\tVerifying FeatureSet",
featureSet.getLocalId(),
"with reference", reference.getLocalId())
length = min(reference.getLength(), 1000)
features = featureSet.getFeatures(
reference.getLocalId(), 0, length, None, 3)
for feature in features:
print("\t{}".format(feature))
# for continuousSet in dataset.getContinuousSets():
# -- there is no getContinuous
for readGroupSet in dataset.getReadGroupSets():
print(
"\tVerifying ReadGroupSet", readGroupSet.getLocalId(),
"@", readGroupSet.getDataUrl())
references = readGroupSet.getReferenceSet().getReferences()
# TODO should we cycle through the references? Should probably
# be an option.
reference = references[0]
max_alignments = 10
for readGroup in readGroupSet.getReadGroups():
alignments = readGroup.getReadAlignments(reference)
for i, alignment in enumerate(alignments):
if i == max_alignments:
break
print(
"\t\tRead", i, "alignments from",
readGroup.getLocalId())
for variantSet in dataset.getVariantSets():
print("\tVerifying VariantSet", variantSet.getLocalId())
max_variants = 10
max_annotations = 10
refMap = variantSet.getReferenceToDataUrlIndexMap()
for referenceName, (dataUrl, indexFile) in refMap.items():
variants = variantSet.getVariants(referenceName, 0, 2**31)
for i, variant in enumerate(variants):
if i == max_variants:
break
print(
"\t\tRead", i, "variants from reference",
referenceName, "@", dataUrl)
for annotationSet in variantSet.getVariantAnnotationSets():
print(
"\t\tVerifying VariantAnnotationSet",
annotationSet.getLocalId())
for referenceName in refMap.keys():
annotations = annotationSet.getVariantAnnotations(
referenceName, 0, 2**31)
for i, annotation in enumerate(annotations):
if i == max_annotations:
break
print(
"\t\t\tRead", i, "annotations from reference",
referenceName)
for phenotypeAssociationSet \
in dataset.getPhenotypeAssociationSets():
print("\t\tVerifying PhenotypeAssociationSet")
print(
"\t\t\t", phenotypeAssociationSet.getLocalId(),
phenotypeAssociationSet.getParentContainer().getId(),
sep="\t") | Verifies that the data in the repository is consistent. | entailment |
def insertOntology(self, ontology):
"""
Inserts the specified ontology into this repository.
"""
try:
models.Ontology.create(
id=ontology.getName(),
name=ontology.getName(),
dataurl=ontology.getDataUrl(),
ontologyprefix=ontology.getOntologyPrefix())
except Exception:
raise exceptions.DuplicateNameException(
ontology.getName()) | Inserts the specified ontology into this repository. | entailment |
def removeOntology(self, ontology):
"""
Removes the specified ontology term map from this repository.
"""
q = models.Ontology.delete().where(id == ontology.getId())
q.execute() | Removes the specified ontology term map from this repository. | entailment |
def insertReference(self, reference):
"""
Inserts the specified reference into this repository.
"""
models.Reference.create(
id=reference.getId(),
referencesetid=reference.getParentContainer().getId(),
name=reference.getLocalId(),
length=reference.getLength(),
isderived=reference.getIsDerived(),
species=json.dumps(reference.getSpecies()),
md5checksum=reference.getMd5Checksum(),
sourceaccessions=json.dumps(reference.getSourceAccessions()),
sourceuri=reference.getSourceUri()) | Inserts the specified reference into this repository. | entailment |
def insertReferenceSet(self, referenceSet):
"""
Inserts the specified referenceSet into this repository.
"""
try:
models.Referenceset.create(
id=referenceSet.getId(),
name=referenceSet.getLocalId(),
description=referenceSet.getDescription(),
assemblyid=referenceSet.getAssemblyId(),
isderived=referenceSet.getIsDerived(),
species=json.dumps(referenceSet.getSpecies()),
md5checksum=referenceSet.getMd5Checksum(),
sourceaccessions=json.dumps(
referenceSet.getSourceAccessions()),
sourceuri=referenceSet.getSourceUri(),
dataurl=referenceSet.getDataUrl())
for reference in referenceSet.getReferences():
self.insertReference(reference)
except Exception:
raise exceptions.DuplicateNameException(
referenceSet.getLocalId()) | Inserts the specified referenceSet into this repository. | entailment |
def insertDataset(self, dataset):
"""
Inserts the specified dataset into this repository.
"""
try:
models.Dataset.create(
id=dataset.getId(),
name=dataset.getLocalId(),
description=dataset.getDescription(),
attributes=json.dumps(dataset.getAttributes()))
except Exception:
raise exceptions.DuplicateNameException(
dataset.getLocalId()) | Inserts the specified dataset into this repository. | entailment |
def removeDataset(self, dataset):
"""
Removes the specified dataset from this repository. This performs
a cascading removal of all items within this dataset.
"""
for datasetRecord in models.Dataset.select().where(
models.Dataset.id == dataset.getId()):
datasetRecord.delete_instance(recursive=True) | Removes the specified dataset from this repository. This performs
a cascading removal of all items within this dataset. | entailment |
def removePhenotypeAssociationSet(self, phenotypeAssociationSet):
"""
Remove a phenotype association set from the repo
"""
q = models.Phenotypeassociationset.delete().where(
models.Phenotypeassociationset.id ==
phenotypeAssociationSet.getId())
q.execute() | Remove a phenotype association set from the repo | entailment |
def removeFeatureSet(self, featureSet):
"""
Removes the specified featureSet from this repository.
"""
q = models.Featureset.delete().where(
models.Featureset.id == featureSet.getId())
q.execute() | Removes the specified featureSet from this repository. | entailment |
def removeContinuousSet(self, continuousSet):
"""
Removes the specified continuousSet from this repository.
"""
q = models.ContinuousSet.delete().where(
models.ContinuousSet.id == continuousSet.getId())
q.execute() | Removes the specified continuousSet from this repository. | entailment |
def insertReadGroup(self, readGroup):
"""
Inserts the specified readGroup into the DB.
"""
statsJson = json.dumps(protocol.toJsonDict(readGroup.getStats()))
experimentJson = json.dumps(
protocol.toJsonDict(readGroup.getExperiment()))
try:
models.Readgroup.create(
id=readGroup.getId(),
readgroupsetid=readGroup.getParentContainer().getId(),
name=readGroup.getLocalId(),
predictedinsertedsize=readGroup.getPredictedInsertSize(),
samplename=readGroup.getSampleName(),
description=readGroup.getDescription(),
stats=statsJson,
experiment=experimentJson,
biosampleid=readGroup.getBiosampleId(),
attributes=json.dumps(readGroup.getAttributes()))
except Exception as e:
raise exceptions.RepoManagerException(e) | Inserts the specified readGroup into the DB. | entailment |
def removeReadGroupSet(self, readGroupSet):
"""
Removes the specified readGroupSet from this repository. This performs
a cascading removal of all items within this readGroupSet.
"""
for readGroupSetRecord in models.Readgroupset.select().where(
models.Readgroupset.id == readGroupSet.getId()):
readGroupSetRecord.delete_instance(recursive=True) | Removes the specified readGroupSet from this repository. This performs
a cascading removal of all items within this readGroupSet. | entailment |
def removeVariantSet(self, variantSet):
"""
Removes the specified variantSet from this repository. This performs
a cascading removal of all items within this variantSet.
"""
for variantSetRecord in models.Variantset.select().where(
models.Variantset.id == variantSet.getId()):
variantSetRecord.delete_instance(recursive=True) | Removes the specified variantSet from this repository. This performs
a cascading removal of all items within this variantSet. | entailment |
def removeBiosample(self, biosample):
"""
Removes the specified biosample from this repository.
"""
q = models.Biosample.delete().where(
models.Biosample.id == biosample.getId())
q.execute() | Removes the specified biosample from this repository. | entailment |
def removeIndividual(self, individual):
"""
Removes the specified individual from this repository.
"""
q = models.Individual.delete().where(
models.Individual.id == individual.getId())
q.execute() | Removes the specified individual from this repository. | entailment |
def insertReadGroupSet(self, readGroupSet):
"""
Inserts a the specified readGroupSet into this repository.
"""
programsJson = json.dumps(
[protocol.toJsonDict(program) for program in
readGroupSet.getPrograms()])
statsJson = json.dumps(protocol.toJsonDict(readGroupSet.getStats()))
try:
models.Readgroupset.create(
id=readGroupSet.getId(),
datasetid=readGroupSet.getParentContainer().getId(),
referencesetid=readGroupSet.getReferenceSet().getId(),
name=readGroupSet.getLocalId(),
programs=programsJson,
stats=statsJson,
dataurl=readGroupSet.getDataUrl(),
indexfile=readGroupSet.getIndexFile(),
attributes=json.dumps(readGroupSet.getAttributes()))
for readGroup in readGroupSet.getReadGroups():
self.insertReadGroup(readGroup)
except Exception as e:
raise exceptions.RepoManagerException(e) | Inserts a the specified readGroupSet into this repository. | entailment |
def removeReferenceSet(self, referenceSet):
"""
Removes the specified referenceSet from this repository. This performs
a cascading removal of all references within this referenceSet.
However, it does not remove any of the ReadGroupSets or items that
refer to this ReferenceSet. These must be deleted before the
referenceSet can be removed.
"""
try:
q = models.Reference.delete().where(
models.Reference.referencesetid == referenceSet.getId())
q.execute()
q = models.Referenceset.delete().where(
models.Referenceset.id == referenceSet.getId())
q.execute()
except Exception:
msg = ("Unable to delete reference set. "
"There are objects currently in the registry which are "
"aligned against it. Remove these objects before removing "
"the reference set.")
raise exceptions.RepoManagerException(msg) | Removes the specified referenceSet from this repository. This performs
a cascading removal of all references within this referenceSet.
However, it does not remove any of the ReadGroupSets or items that
refer to this ReferenceSet. These must be deleted before the
referenceSet can be removed. | entailment |
def insertVariantAnnotationSet(self, variantAnnotationSet):
"""
Inserts a the specified variantAnnotationSet into this repository.
"""
analysisJson = json.dumps(
protocol.toJsonDict(variantAnnotationSet.getAnalysis()))
try:
models.Variantannotationset.create(
id=variantAnnotationSet.getId(),
variantsetid=variantAnnotationSet.getParentContainer().getId(),
ontologyid=variantAnnotationSet.getOntology().getId(),
name=variantAnnotationSet.getLocalId(),
analysis=analysisJson,
annotationtype=variantAnnotationSet.getAnnotationType(),
created=variantAnnotationSet.getCreationTime(),
updated=variantAnnotationSet.getUpdatedTime(),
attributes=json.dumps(variantAnnotationSet.getAttributes()))
except Exception as e:
raise exceptions.RepoManagerException(e) | Inserts a the specified variantAnnotationSet into this repository. | entailment |
def insertCallSet(self, callSet):
"""
Inserts a the specified callSet into this repository.
"""
try:
models.Callset.create(
id=callSet.getId(),
name=callSet.getLocalId(),
variantsetid=callSet.getParentContainer().getId(),
biosampleid=callSet.getBiosampleId(),
attributes=json.dumps(callSet.getAttributes()))
except Exception as e:
raise exceptions.RepoManagerException(e) | Inserts a the specified callSet into this repository. | entailment |
def insertVariantSet(self, variantSet):
"""
Inserts a the specified variantSet into this repository.
"""
# We cheat a little here with the VariantSetMetadata, and encode these
# within the table as a JSON dump. These should really be stored in
# their own table
metadataJson = json.dumps(
[protocol.toJsonDict(metadata) for metadata in
variantSet.getMetadata()])
urlMapJson = json.dumps(variantSet.getReferenceToDataUrlIndexMap())
try:
models.Variantset.create(
id=variantSet.getId(),
datasetid=variantSet.getParentContainer().getId(),
referencesetid=variantSet.getReferenceSet().getId(),
name=variantSet.getLocalId(),
created=datetime.datetime.now(),
updated=datetime.datetime.now(),
metadata=metadataJson,
dataurlindexmap=urlMapJson,
attributes=json.dumps(variantSet.getAttributes()))
except Exception as e:
raise exceptions.RepoManagerException(e)
for callSet in variantSet.getCallSets():
self.insertCallSet(callSet) | Inserts a the specified variantSet into this repository. | entailment |
def insertFeatureSet(self, featureSet):
"""
Inserts a the specified featureSet into this repository.
"""
# TODO add support for info and sourceUri fields.
try:
models.Featureset.create(
id=featureSet.getId(),
datasetid=featureSet.getParentContainer().getId(),
referencesetid=featureSet.getReferenceSet().getId(),
ontologyid=featureSet.getOntology().getId(),
name=featureSet.getLocalId(),
dataurl=featureSet.getDataUrl(),
attributes=json.dumps(featureSet.getAttributes()))
except Exception as e:
raise exceptions.RepoManagerException(e) | Inserts a the specified featureSet into this repository. | entailment |
def insertContinuousSet(self, continuousSet):
"""
Inserts a the specified continuousSet into this repository.
"""
# TODO add support for info and sourceUri fields.
try:
models.ContinuousSet.create(
id=continuousSet.getId(),
datasetid=continuousSet.getParentContainer().getId(),
referencesetid=continuousSet.getReferenceSet().getId(),
name=continuousSet.getLocalId(),
dataurl=continuousSet.getDataUrl(),
attributes=json.dumps(continuousSet.getAttributes()))
except Exception as e:
raise exceptions.RepoManagerException(e) | Inserts a the specified continuousSet into this repository. | entailment |
def insertBiosample(self, biosample):
"""
Inserts the specified Biosample into this repository.
"""
try:
models.Biosample.create(
id=biosample.getId(),
datasetid=biosample.getParentContainer().getId(),
name=biosample.getLocalId(),
description=biosample.getDescription(),
disease=json.dumps(biosample.getDisease()),
created=biosample.getCreated(),
updated=biosample.getUpdated(),
individualid=biosample.getIndividualId(),
attributes=json.dumps(biosample.getAttributes()),
individualAgeAtCollection=json.dumps(
biosample.getIndividualAgeAtCollection()))
except Exception:
raise exceptions.DuplicateNameException(
biosample.getLocalId(),
biosample.getParentContainer().getLocalId()) | Inserts the specified Biosample into this repository. | entailment |
def insertIndividual(self, individual):
"""
Inserts the specified individual into this repository.
"""
try:
models.Individual.create(
id=individual.getId(),
datasetId=individual.getParentContainer().getId(),
name=individual.getLocalId(),
description=individual.getDescription(),
created=individual.getCreated(),
updated=individual.getUpdated(),
species=json.dumps(individual.getSpecies()),
sex=json.dumps(individual.getSex()),
attributes=json.dumps(individual.getAttributes()))
except Exception:
raise exceptions.DuplicateNameException(
individual.getLocalId(),
individual.getParentContainer().getLocalId()) | Inserts the specified individual into this repository. | entailment |
def insertPhenotypeAssociationSet(self, phenotypeAssociationSet):
"""
Inserts the specified phenotype annotation set into this repository.
"""
datasetId = phenotypeAssociationSet.getParentContainer().getId()
attributes = json.dumps(phenotypeAssociationSet.getAttributes())
try:
models.Phenotypeassociationset.create(
id=phenotypeAssociationSet.getId(),
name=phenotypeAssociationSet.getLocalId(),
datasetid=datasetId,
dataurl=phenotypeAssociationSet._dataUrl,
attributes=attributes)
except Exception:
raise exceptions.DuplicateNameException(
phenotypeAssociationSet.getParentContainer().getId()) | Inserts the specified phenotype annotation set into this repository. | entailment |
def insertRnaQuantificationSet(self, rnaQuantificationSet):
"""
Inserts a the specified rnaQuantificationSet into this repository.
"""
try:
models.Rnaquantificationset.create(
id=rnaQuantificationSet.getId(),
datasetid=rnaQuantificationSet.getParentContainer().getId(),
referencesetid=rnaQuantificationSet.getReferenceSet().getId(),
name=rnaQuantificationSet.getLocalId(),
dataurl=rnaQuantificationSet.getDataUrl(),
attributes=json.dumps(rnaQuantificationSet.getAttributes()))
except Exception:
raise exceptions.DuplicateNameException(
rnaQuantificationSet.getLocalId(),
rnaQuantificationSet.getParentContainer().getLocalId()) | Inserts a the specified rnaQuantificationSet into this repository. | entailment |
def removeRnaQuantificationSet(self, rnaQuantificationSet):
"""
Removes the specified rnaQuantificationSet from this repository. This
performs a cascading removal of all items within this
rnaQuantificationSet.
"""
q = models.Rnaquantificationset.delete().where(
models.Rnaquantificationset.id == rnaQuantificationSet.getId())
q.execute() | Removes the specified rnaQuantificationSet from this repository. This
performs a cascading removal of all items within this
rnaQuantificationSet. | entailment |
def insertPeer(self, peer):
"""
Accepts a peer datamodel object and adds it to the registry.
"""
try:
models.Peer.create(
url=peer.getUrl(),
attributes=json.dumps(peer.getAttributes()))
except Exception as e:
raise exceptions.RepoManagerException(e) | Accepts a peer datamodel object and adds it to the registry. | entailment |
def removePeer(self, url):
"""
Remove peers by URL.
"""
q = models.Peer.delete().where(
models.Peer.url == url)
q.execute() | Remove peers by URL. | entailment |
def initialise(self):
"""
Initialise this data repository, creating any necessary directories
and file paths.
"""
self._checkWriteMode()
self._createSystemTable()
self._createNetworkTables()
self._createOntologyTable()
self._createReferenceSetTable()
self._createReferenceTable()
self._createDatasetTable()
self._createReadGroupSetTable()
self._createReadGroupTable()
self._createCallSetTable()
self._createVariantSetTable()
self._createVariantAnnotationSetTable()
self._createFeatureSetTable()
self._createContinuousSetTable()
self._createBiosampleTable()
self._createIndividualTable()
self._createPhenotypeAssociationSetTable()
self._createRnaQuantificationSetTable() | Initialise this data repository, creating any necessary directories
and file paths. | entailment |
def load(self):
"""
Loads this data repository into memory.
"""
self._readSystemTable()
self._readOntologyTable()
self._readReferenceSetTable()
self._readReferenceTable()
self._readDatasetTable()
self._readReadGroupSetTable()
self._readReadGroupTable()
self._readVariantSetTable()
self._readCallSetTable()
self._readVariantAnnotationSetTable()
self._readFeatureSetTable()
self._readContinuousSetTable()
self._readBiosampleTable()
self._readIndividualTable()
self._readPhenotypeAssociationSetTable()
self._readRnaQuantificationSetTable() | Loads this data repository into memory. | entailment |
def populateFromRow(self, featureSetRecord):
"""
Populates the instance variables of this FeatureSet from the specified
DB row.
"""
self._dbFilePath = featureSetRecord.dataurl
self.setAttributesJson(featureSetRecord.attributes)
self.populateFromFile(self._dbFilePath) | Populates the instance variables of this FeatureSet from the specified
DB row. | entailment |
def populateFromFile(self, dataUrl):
"""
Populates the instance variables of this FeatureSet from the specified
data URL.
Initialize dataset, using the passed dict of sources
[{source,format}] see rdflib.parse() for more
If path is set, this backend will load itself
"""
self._dbFilePath = dataUrl
# initialize graph
self._rdfGraph = rdflib.ConjunctiveGraph()
# save the path
self._dataUrl = dataUrl
self._scanDataFiles(self._dataUrl, ['*.ttl'])
# extract version
cgdTTL = rdflib.URIRef("http://data.monarchinitiative.org/ttl/cgd.ttl")
versionInfo = rdflib.URIRef(
u'http://www.w3.org/2002/07/owl#versionInfo')
self._version = None
for _, _, obj in self._rdfGraph.triples((cgdTTL, versionInfo, None)):
self._version = obj.toPython()
# setup location cache
self._initializeLocationCache() | Populates the instance variables of this FeatureSet from the specified
data URL.
Initialize dataset, using the passed dict of sources
[{source,format}] see rdflib.parse() for more
If path is set, this backend will load itself | entailment |
def getFeature(self, compoundId):
"""
find a feature and return ga4gh representation, use compoundId as
featureId
"""
feature = self._getFeatureById(compoundId.featureId)
feature.id = str(compoundId)
return feature | find a feature and return ga4gh representation, use compoundId as
featureId | entailment |
def _getFeatureById(self, featureId):
"""
find a feature and return ga4gh representation, use 'native' id as
featureId
"""
featureRef = rdflib.URIRef(featureId)
featureDetails = self._detailTuples([featureRef])
feature = {}
for detail in featureDetails:
feature[detail['predicate']] = []
for detail in featureDetails:
feature[detail['predicate']].append(detail['object'])
pbFeature = protocol.Feature()
term = protocol.OntologyTerm()
# Schema for feature only supports one type of `type`
# here we default to first OBO defined
for featureType in sorted(feature[TYPE]):
if "obolibrary" in featureType:
term.term = self._featureTypeLabel(featureType)
term.term_id = featureType
pbFeature.feature_type.MergeFrom(term)
break
pbFeature.id = featureId
# Schema for feature only supports one type of `name` `symbol`
# here we default to shortest for symbol and longest for name
feature[LABEL].sort(key=len)
pbFeature.gene_symbol = feature[LABEL][0]
pbFeature.name = feature[LABEL][-1]
pbFeature.attributes.MergeFrom(protocol.Attributes())
for key in feature:
for val in sorted(feature[key]):
pbFeature.attributes.attr[key].values.add().string_value = val
if featureId in self._locationMap:
location = self._locationMap[featureId]
pbFeature.reference_name = location["chromosome"]
pbFeature.start = location["begin"]
pbFeature.end = location["end"]
return pbFeature | find a feature and return ga4gh representation, use 'native' id as
featureId | entailment |
def _filterSearchFeaturesRequest(self, reference_name, gene_symbol, name,
start, end):
"""
formulate a sparql query string based on parameters
"""
filters = []
query = self._baseQuery()
filters = []
location = self._findLocation(reference_name, start, end)
if location:
filters.append("?feature = <{}>".format(location))
if gene_symbol:
filters.append('regex(?feature_label, "{}")')
if name:
filters.append(
'regex(?feature_label, "{}")'.format(name))
# apply filters
filter = "FILTER ({})".format(' && '.join(filters))
if len(filters) == 0:
filter = ""
query = query.replace("#%FILTER%", filter)
return query | formulate a sparql query string based on parameters | entailment |
def _findLocation(self, reference_name, start, end):
"""
return a location key form the locationMap
"""
try:
# TODO - sequence_annotations does not have build?
return self._locationMap['hg19'][reference_name][start][end]
except:
return None | return a location key form the locationMap | entailment |
def _initializeLocationCache(self):
"""
CGD uses Faldo ontology for locations, it's a bit complicated.
This function sets up an in memory cache of all locations, which
can be queried via:
locationMap[build][chromosome][begin][end] = location["_id"]
"""
# cache of locations
self._locationMap = {}
locationMap = self._locationMap
triples = self._rdfGraph.triples
Ref = rdflib.URIRef
associations = []
for subj, _, _ in triples((None, RDF.type, Ref(ASSOCIATION))):
associations.append(subj.toPython())
locationIds = []
for association in associations:
for _, _, obj in triples((Ref(association),
Ref(HAS_SUBJECT), None)):
locationIds.append(obj.toPython())
locations = []
for _id in locationIds:
location = {}
location["_id"] = _id
for subj, predicate, obj in triples((Ref(location["_id"]),
None, None)):
if not predicate.toPython() in location:
location[predicate.toPython()] = []
bisect.insort(location[predicate.toPython()], obj.toPython())
if FALDO_LOCATION in location:
locations.append(location)
for location in locations:
for _id in location[FALDO_LOCATION]:
# lookup faldo region, ensure positions are sorted
faldoLocation = {}
faldoLocation["_id"] = _id
for subj, predicate, obj in triples((Ref(faldoLocation["_id"]),
None, None)):
if not predicate.toPython() in faldoLocation:
faldoLocation[predicate.toPython()] = []
bisect.insort(faldoLocation[predicate.toPython()],
obj.toPython())
faldoBegins = []
for _id in faldoLocation[FALDO_BEGIN]:
faldoBegin = {}
faldoBegin["_id"] = _id
for subj, predicate, obj in triples(
(Ref(faldoBegin["_id"]),
None, None)):
faldoBegin[predicate.toPython()] = obj.toPython()
faldoBegins.append(faldoBegin)
faldoReferences = []
for _id in faldoLocation[FALDO_BEGIN]:
faldoReference = {}
faldoReference["_id"] = faldoBegin[FALDO_REFERENCE]
for subj, predicate, obj in triples(
(Ref(faldoReference["_id"]),
None, None)):
faldoReference[predicate.toPython()] = obj.toPython()
faldoReferences.append(faldoReference)
faldoEnds = []
for _id in faldoLocation[FALDO_END]:
faldoEnd = {}
faldoEnd["_id"] = _id
for subj, predicate, obj in triples((Ref(faldoEnd["_id"]),
None, None)):
faldoEnd[predicate.toPython()] = obj.toPython()
faldoEnds.append(faldoEnd)
for idx, faldoReference in enumerate(faldoReferences):
if MEMBER_OF in faldoReference:
build = faldoReference[MEMBER_OF].split('/')[-1]
chromosome = faldoReference[LABEL].split(' ')[0]
begin = faldoBegins[idx][FALDO_POSITION]
end = faldoEnds[idx][FALDO_POSITION]
if build not in locationMap:
locationMap[build] = {}
if chromosome not in locationMap[build]:
locationMap[build][chromosome] = {}
if begin not in locationMap[build][chromosome]:
locationMap[build][chromosome][begin] = {}
if end not in locationMap[build][chromosome][begin]:
locationMap[build][chromosome][begin][end] = {}
locationMap[build][chromosome][begin][end] = \
location["_id"]
locationMap[location["_id"]] = {
"build": build,
"chromosome": chromosome,
"begin": begin,
"end": end,
} | CGD uses Faldo ontology for locations, it's a bit complicated.
This function sets up an in memory cache of all locations, which
can be queried via:
locationMap[build][chromosome][begin][end] = location["_id"] | entailment |
def addValue(self, protocolElement):
"""
Appends the specified protocolElement to the value list for this
response.
"""
self._numElements += 1
self._bufferSize += protocolElement.ByteSize()
attr = getattr(self._protoObject, self._valueListName)
obj = attr.add()
obj.CopyFrom(protocolElement) | Appends the specified protocolElement to the value list for this
response. | entailment |
def isFull(self):
"""
Returns True if the response buffer is full, and False otherwise.
The buffer is full if either (1) the number of items in the value
list is >= pageSize or (2) the total length of the serialised
elements in the page is >= maxBufferSize.
If page_size or max_response_length were not set in the request
then they're not checked.
"""
return (
(self._pageSize > 0 and self._numElements >= self._pageSize) or
(self._bufferSize >= self._maxBufferSize)
) | Returns True if the response buffer is full, and False otherwise.
The buffer is full if either (1) the number of items in the value
list is >= pageSize or (2) the total length of the serialised
elements in the page is >= maxBufferSize.
If page_size or max_response_length were not set in the request
then they're not checked. | entailment |
def getSerializedResponse(self):
"""
Returns a string version of the SearchResponse that has
been built by this SearchResponseBuilder.
"""
self._protoObject.next_page_token = pb.string(self._nextPageToken)
s = protocol.toJson(self._protoObject)
return s | Returns a string version of the SearchResponse that has
been built by this SearchResponseBuilder. | entailment |
def populateFromRow(self, ontologyRecord):
"""
Populates this Ontology using values in the specified DB row.
"""
self._id = ontologyRecord.id
self._dataUrl = ontologyRecord.dataurl
self._readFile() | Populates this Ontology using values in the specified DB row. | entailment |
def getGaTermByName(self, name):
"""
Returns a GA4GH OntologyTerm object by name.
:param name: name of the ontology term, ex. "gene".
:return: GA4GH OntologyTerm object.
"""
# TODO what is the correct value when we have no mapping??
termIds = self.getTermIds(name)
if len(termIds) == 0:
termId = ""
# TODO add logging for missed term translation.
else:
# TODO what is the correct behaviour here when we have multiple
# IDs matching a given name?
termId = termIds[0]
term = protocol.OntologyTerm()
term.term = name
term.term_id = termId
return term | Returns a GA4GH OntologyTerm object by name.
:param name: name of the ontology term, ex. "gene".
:return: GA4GH OntologyTerm object. | entailment |
def _heavyQuery(variantSetId, callSetIds):
"""
Very heavy query: calls for the specified list of callSetIds
on chromosome 2 (11 pages, 90 seconds to fetch the entire thing
on a high-end desktop machine)
"""
request = protocol.SearchVariantsRequest()
request.reference_name = '2'
request.variant_set_id = variantSetId
for callSetId in callSetIds:
request.call_set_ids.add(callSetId)
request.page_size = 100
request.end = 100000
return request | Very heavy query: calls for the specified list of callSetIds
on chromosome 2 (11 pages, 90 seconds to fetch the entire thing
on a high-end desktop machine) | entailment |
def timeOneSearch(queryString):
"""
Returns (search result as JSON string, time elapsed during search)
"""
startTime = time.clock()
resultString = backend.runSearchVariants(queryString)
endTime = time.clock()
elapsedTime = endTime - startTime
return resultString, elapsedTime | Returns (search result as JSON string, time elapsed during search) | entailment |
def benchmarkOneQuery(request, repeatLimit=3, pageLimit=3):
"""
Repeat the query several times; perhaps don't go through *all* the
pages. Returns minimum time to run backend.searchVariants() to execute
the query (as far as pageLimit allows), *not* including JSON
processing to prepare queries or parse responses.
"""
times = []
queryString = protocol.toJson(request)
for i in range(0, repeatLimit):
resultString, elapsedTime = timeOneSearch(queryString)
accruedTime = elapsedTime
pageCount = 1
token = extractNextPageToken(resultString)
# Iterate to go beyond the first page of results.
while token is not None and pageCount < pageLimit:
pageRequest = request
pageRequest.page_token = token
pageRequestString = protocol.toJson(pageRequest)
resultString, elapsedTime = timeOneSearch(pageRequestString)
accruedTime += elapsedTime
pageCount = pageCount + 1
token = extractNextPageToken(resultString)
times.append(accruedTime)
# TODO: more sophisticated statistics. Sometimes we want min(),
# sometimes mean = sum() / len(), sometimes other measures,
# perhaps exclude outliers...
# If we compute average we should throw out at least the first one.
# return sum(times[2:])/len(times[2:])
return min(times) | Repeat the query several times; perhaps don't go through *all* the
pages. Returns minimum time to run backend.searchVariants() to execute
the query (as far as pageLimit allows), *not* including JSON
processing to prepare queries or parse responses. | entailment |
def getExceptionClass(errorCode):
"""
Converts the specified error code into the corresponding class object.
Raises a KeyError if the errorCode is not found.
"""
classMap = {}
for name, class_ in inspect.getmembers(sys.modules[__name__]):
if inspect.isclass(class_) and issubclass(class_, BaseServerException):
classMap[class_.getErrorCode()] = class_
return classMap[errorCode] | Converts the specified error code into the corresponding class object.
Raises a KeyError if the errorCode is not found. | entailment |
def toProtocolElement(self):
"""
Converts this exception into the GA4GH protocol type so that
it can be communicated back to the client.
"""
error = protocol.GAException()
error.error_code = self.getErrorCode()
error.message = self.getMessage()
return error | Converts this exception into the GA4GH protocol type so that
it can be communicated back to the client. | entailment |
def _init_goterm_ref(self, rec_curr, name, lnum):
"""Initialize new reference and perform checks."""
if rec_curr is None:
return GOTerm()
msg = "PREVIOUS {REC} WAS NOT TERMINATED AS EXPECTED".format(REC=name)
self._die(msg, lnum) | Initialize new reference and perform checks. | entailment |
def _init_typedef(self, typedef_curr, name, lnum):
"""Initialize new typedef and perform checks."""
if typedef_curr is None:
return TypeDef()
msg = "PREVIOUS {REC} WAS NOT TERMINATED AS EXPECTED".format(REC=name)
self._die(msg, lnum) | Initialize new typedef and perform checks. | entailment |
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