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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | OBOReader._add_to_ref | def _add_to_ref(self, rec_curr, line, lnum):
"""Add new fields to the current reference."""
# Written by DV Klopfenstein
# Examples of record lines containing ':' include:
# id: GO:0000002
# name: mitochondrial genome maintenance
# namespace: biological_process
... | python | def _add_to_ref(self, rec_curr, line, lnum):
"""Add new fields to the current reference."""
# Written by DV Klopfenstein
# Examples of record lines containing ':' include:
# id: GO:0000002
# name: mitochondrial genome maintenance
# namespace: biological_process
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | OBOReader.update_rec | def update_rec(self, rec, name, value):
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | OBOReader._add_to_typedef | def _add_to_typedef(self, typedef_curr, line, lnum):
"""Add new fields to the current typedef."""
mtch = re.match(r'^(\S+):\s*(\S.*)$', line)
if mtch:
field_name = mtch.group(1)
field_value = mtch.group(2).split('!')[0].rstrip()
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... | python | def _add_to_typedef(self, typedef_curr, line, lnum):
"""Add new fields to the current typedef."""
mtch = re.match(r'^(\S+):\s*(\S.*)$', line)
if mtch:
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | OBOReader._add_nested | def _add_nested(self, rec, name, value):
"""Adds a term's nested attributes."""
# Remove comments and split term into typedef / target term.
(typedef, target_term) = value.split('!')[0].rstrip().split(' ')
# Save the nested term.
getattr(rec, name)[typedef].append(target_term) | python | def _add_nested(self, rec, name, value):
"""Adds a term's nested attributes."""
# Remove comments and split term into typedef / target term.
(typedef, target_term) = value.split('!')[0].rstrip().split(' ')
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | OBOReader._init_optional_attrs | def _init_optional_attrs(self, optional_attrs):
"""Prepare to store data from user-desired optional fields.
Not loading these optional fields by default saves in space and speed.
But allow the possibility for saving these fields, if the user desires,
Including:
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | OBOReader._die | def _die(self, msg, lnum):
"""Raise an Exception if file read is unexpected."""
raise Exception("**FATAL {FILE}({LNUM}): {MSG}\n".format(
FILE=self.obo_file, LNUM=lnum, MSG=msg)) | python | def _die(self, msg, lnum):
"""Raise an Exception if file read is unexpected."""
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | GOTerm.write_hier_rec | def write_hier_rec(self, gos_printed, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False,
include_only=None, go_marks=None,
depth=1, dp="-"):
"""Write hierarchy for a GO Term record."""
# Added by DV Klopfenstein
... | python | def write_hier_rec(self, gos_printed, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False,
include_only=None, go_marks=None,
depth=1, dp="-"):
"""Write hierarchy for a GO Term record."""
# Added by DV Klopfenstein
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | GODag.write_hier_all | def write_hier_all(self, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False):
"""Write hierarchy for all GO Terms in obo file."""
# Print: [biological_process, molecular_function, and cellular_component]
for go_id in ['GO:0008150', 'GO:0003674', 'GO... | python | def write_hier_all(self, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False):
"""Write hierarchy for all GO Terms in obo file."""
# Print: [biological_process, molecular_function, and cellular_component]
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | GODag.write_hier | def write_hier(self, GO_id, out=sys.stdout,
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include_only=None, go_marks=None):
"""Write hierarchy for a GO Term."""
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include_only=None, go_marks=None):
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | GODag.paths_to_top | def paths_to_top(self, term):
""" Returns all possible paths to the root node
Each path includes the term given. The order of the path is
top -> bottom, i.e. it starts with the root and ends with the
given term (inclusively).
Parameters:
-----------
... | python | def paths_to_top(self, term):
""" Returns all possible paths to the root node
Each path includes the term given. The order of the path is
top -> bottom, i.e. it starts with the root and ends with the
given term (inclusively).
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ga4gh/ga4gh-server | ga4gh/server/datamodel/obo_parser.py | GODag.make_graph_pydot | def make_graph_pydot(self, recs, nodecolor,
edgecolor, dpi,
draw_parents=True, draw_children=True):
"""draw AMIGO style network, lineage containing one query record."""
import pydot
G = pydot.Dot(graph_type='digraph', dpi="{}".format(dpi)) # Directed Gra... | python | def make_graph_pydot(self, recs, nodecolor,
edgecolor, dpi,
draw_parents=True, draw_children=True):
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ga4gh/ga4gh-server | ga4gh/server/sqlite_backend.py | sqliteRowsToDicts | def sqliteRowsToDicts(sqliteRows):
"""
Unpacks sqlite rows as returned by fetchall
into an array of simple dicts.
:param sqliteRows: array of rows returned from fetchall DB call
:return: array of dicts, keyed by the column names.
"""
return map(lambda r: dict(zip(r.keys(), r)), sqliteRows) | python | def sqliteRowsToDicts(sqliteRows):
"""
Unpacks sqlite rows as returned by fetchall
into an array of simple dicts.
:param sqliteRows: array of rows returned from fetchall DB call
:return: array of dicts, keyed by the column names.
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ga4gh/ga4gh-server | ga4gh/server/sqlite_backend.py | limitsSql | def limitsSql(startIndex=0, maxResults=0):
"""
Construct a SQL LIMIT clause
"""
if startIndex and maxResults:
return " LIMIT {}, {}".format(startIndex, maxResults)
elif startIndex:
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"""
Construct a SQL LIMIT clause
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ga4gh/ga4gh-server | ga4gh/server/sqlite_backend.py | iterativeFetch | def iterativeFetch(query, batchSize=default_batch_size):
"""
Returns rows of a sql fetch query on demand
"""
while True:
rows = query.fetchmany(batchSize)
if not rows:
break
rowDicts = sqliteRowsToDicts(rows)
for rowDict in rowDicts:
yield rowDict | python | def iterativeFetch(query, batchSize=default_batch_size):
"""
Returns rows of a sql fetch query on demand
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rows = query.fetchmany(batchSize)
if not rows:
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rowDicts = sqliteRowsToDicts(rows)
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ga4gh/ga4gh-server | ga4gh/server/paging.py | _parsePageToken | def _parsePageToken(pageToken, numValues):
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ga4gh/ga4gh-server | ga4gh/server/paging.py | _parseIntegerArgument | def _parseIntegerArgument(args, key, defaultValue):
"""
Attempts to parse the specified key in the specified argument
dictionary into an integer. If the argument cannot be parsed,
raises a BadRequestIntegerException. If the key is not present,
return the specified default value.
"""
ret = de... | python | def _parseIntegerArgument(args, key, defaultValue):
"""
Attempts to parse the specified key in the specified argument
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ga4gh/ga4gh-server | ga4gh/server/paging.py | IntervalIterator._initialiseIteration | def _initialiseIteration(self):
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ga4gh/ga4gh-server | ga4gh/server/paging.py | IntervalIterator._pickUpIteration | def _pickUpIteration(self, searchAnchor, objectsToSkip):
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ga4gh/ga4gh-server | ga4gh/server/paging.py | IntervalIterator.next | def next(self):
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ga4gh/ga4gh-server | ga4gh/server/paging.py | VariantAnnotationsIntervalIterator.filterVariantAnnotation | def filterVariantAnnotation(self, vann):
"""
Returns true when an annotation should be included.
"""
# TODO reintroduce feature ID search
ret = False
if len(self._effects) != 0 and not vann.transcript_effects:
return False
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"""
Returns true when an annotation should be included.
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ga4gh/ga4gh-server | ga4gh/server/paging.py | VariantAnnotationsIntervalIterator.filterEffect | def filterEffect(self, teff):
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ga4gh/ga4gh-server | ga4gh/server/paging.py | VariantAnnotationsIntervalIterator._checkIdEquality | def _checkIdEquality(self, requestedEffect, effect):
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ga4gh/ga4gh-server | scripts/glue.py | ga4ghImportGlue | def ga4ghImportGlue():
"""
Call this method before importing a ga4gh module in the scripts dir.
Otherwise, you will be using the installed package instead of
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | PysamFileHandleCache._update | def _update(self, dataFile, handle):
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | CompoundId.join | def join(cls, splits):
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | DatamodelObject.serializeAttributes | def serializeAttributes(self, msg):
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | DatamodelObject._scanDataFiles | def _scanDataFiles(self, dataDir, patterns):
"""
Scans the specified directory for files with the specified globbing
pattern and calls self._addDataFile for each. Raises an
EmptyDirException if no data files are found.
"""
numDataFiles = 0
for pattern in patterns:... | python | def _scanDataFiles(self, dataDir, patterns):
"""
Scans the specified directory for files with the specified globbing
pattern and calls self._addDataFile for each. Raises an
EmptyDirException if no data files are found.
"""
numDataFiles = 0
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ga4gh/ga4gh-server | ga4gh/server/network/__init__.py | getInitialPeerList | def getInitialPeerList(filePath, logger=None):
"""
Attempts to get a list of peers from a file specified in configuration.
This file has one URL per line and can contain newlines and comments.
# Main ga4gh node
http://1kgenomes.ga4gh.org
# Local intranet peer
https://192.16... | python | def getInitialPeerList(filePath, logger=None):
"""
Attempts to get a list of peers from a file specified in configuration.
This file has one URL per line and can contain newlines and comments.
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http://1kgenomes.ga4gh.org
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ga4gh/ga4gh-server | ga4gh/server/network/__init__.py | insertInitialPeer | def insertInitialPeer(dataRepository, url, logger=None):
"""
Takes the datarepository, a url, and an optional logger and attempts
to add the peer into the repository.
"""
insertPeer = dataRepository.insertPeer
try:
peer = datamodel.peers.Peer(url)
insertPeer(peer)
except exce... | python | def insertInitialPeer(dataRepository, url, logger=None):
"""
Takes the datarepository, a url, and an optional logger and attempts
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"""
insertPeer = dataRepository.insertPeer
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ga4gh/ga4gh-server | ga4gh/server/datamodel/peers.py | isUrl | def isUrl(urlString):
"""
Attempts to return whether a given URL string is valid by checking
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From http://stackoverflow.com/questions/7160737/
"""
parsed = urlparse.urlparse(urlString)
urlpar... | python | def isUrl(urlString):
"""
Attempts to return whether a given URL string is valid by checking
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ga4gh/ga4gh-server | ga4gh/server/datamodel/peers.py | Peer.setUrl | 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 | python | def setUrl(self, url):
"""
Attempt to safely set the URL by string.
"""
if isUrl(url):
self._url = url
else:
raise exceptions.BadUrlException(url)
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ga4gh/ga4gh-server | ga4gh/server/datamodel/peers.py | Peer.setAttributesJson | 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 | python | def setAttributesJson(self, attributesJson):
"""
Sets the attributes dictionary from a JSON string.
"""
try:
self._attributes = json.loads(attributesJson)
except:
raise exceptions.InvalidJsonException(attributesJson)
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ga4gh/ga4gh-server | ga4gh/server/datamodel/peers.py | Peer.populateFromRow | def populateFromRow(self, peerRecord):
"""
This method accepts a model record and sets class variables.
"""
self.setUrl(peerRecord.url) \
.setAttributesJson(peerRecord.attributes)
return self | python | def populateFromRow(self, peerRecord):
"""
This method accepts a model record and sets class variables.
"""
self.setUrl(peerRecord.url) \
.setAttributesJson(peerRecord.attributes)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend._topLevelObjectGenerator | def _topLevelObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
... | python | def _topLevelObjectGenerator(self, request, numObjects, getByIndexMethod):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend._protocolObjectGenerator | def _protocolObjectGenerator(self, request, numObjects, getByIndexMethod):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend._protocolListGenerator | def _protocolListGenerator(self, request, objectList):
"""
Returns a generator over the objects in the specified list using
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"""
return self._protocolObjectGenerator(
request, len(objectList), lambda index: objectList[i... | python | def _protocolListGenerator(self, request, objectList):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend._objectListGenerator | def _objectListGenerator(self, request, objectList):
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.datasetsGenerator | def datasetsGenerator(self, request):
"""
Returns a generator over the (dataset, nextPageToken) pairs
defined by the specified request
"""
return self._topLevelObjectGenerator(
request, self.getDataRepository().getNumDatasets(),
self.getDataRepository().ge... | python | def datasetsGenerator(self, request):
"""
Returns a generator over the (dataset, nextPageToken) pairs
defined by the specified request
"""
return self._topLevelObjectGenerator(
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.phenotypeAssociationSetsGenerator | def phenotypeAssociationSetsGenerator(self, request):
"""
Returns a generator over the (phenotypeAssociationSet, nextPageToken)
pairs defined by the specified request
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerato... | python | def phenotypeAssociationSetsGenerator(self, request):
"""
Returns a generator over the (phenotypeAssociationSet, nextPageToken)
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"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.readGroupSetsGenerator | def readGroupSetsGenerator(self, request):
"""
Returns a generator over the (readGroupSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._readGroupSetsGenerator(
request... | python | def readGroupSetsGenerator(self, request):
"""
Returns a generator over the (readGroupSet, nextPageToken) pairs
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"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend._readGroupSetsGenerator | def _readGroupSetsGenerator(self, request, numObjects, getByIndexMethod):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.referenceSetsGenerator | def referenceSetsGenerator(self, request):
"""
Returns a generator over the (referenceSet, nextPageToken) pairs
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"""
results = []
for obj in self.getDataRepository().getReferenceSets():
include = True
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.referencesGenerator | def referencesGenerator(self, request):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.variantSetsGenerator | def variantSetsGenerator(self, request):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.variantAnnotationSetsGenerator | def variantAnnotationSetsGenerator(self, request):
"""
Returns a generator over the (variantAnnotationSet, nextPageToken)
pairs defined by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
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dataset = self.getD... | python | def variantAnnotationSetsGenerator(self, request):
"""
Returns a generator over the (variantAnnotationSet, nextPageToken)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.readsGenerator | def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
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"""
if not request.reference_id:
raise exceptions.UnmappedReadsNotSupported()
if len(request.read_group_ids) < 1:
raise... | python | def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.variantsGenerator | def variantsGenerator(self, request):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.variantAnnotationsGenerator | def variantAnnotationsGenerator(self, request):
"""
Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
defined by the specified request.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(
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dat... | python | def variantAnnotationsGenerator(self, request):
"""
Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
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compoundId = datamodel.VariantAnnotationSetCompoundId.parse(
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.featuresGenerator | def featuresGenerator(self, request):
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Returns a generator over the (features, nextPageToken) pairs
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"""
compoundId = None
parentId = None
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compoundId = datamodel.FeatureSetCompoun... | python | def featuresGenerator(self, request):
"""
Returns a generator over the (features, nextPageToken) pairs
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compoundId = None
parentId = None
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.continuousGenerator | def continuousGenerator(self, request):
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Returns a generator over the (continuous, nextPageToken) pairs
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compoundId = None
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"""
Returns a generator over the (continuous, nextPageToken) pairs
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compoundId = None
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.phenotypesGenerator | def phenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
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"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.genotypesPhenotypesGenerator | def genotypesPhenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
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"""
Returns a generator over the (phenotypes, nextPageToken) pairs
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# TODO make paging work using SPARQL?
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.callSetsGenerator | def callSetsGenerator(self, request):
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Returns a generator over the (callSet, nextPageToken) pairs defined
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"""
compoundId = datamodel.VariantSetCompoundId.parse(
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dataset = self.getDataRepository().getDataset... | python | def callSetsGenerator(self, request):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.featureSetsGenerator | def featureSetsGenerator(self, request):
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"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.continuousSetsGenerator | def continuousSetsGenerator(self, request):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.rnaQuantificationSetsGenerator | def rnaQuantificationSetsGenerator(self, request):
"""
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"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
... | python | def rnaQuantificationSetsGenerator(self, request):
"""
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dataset = self.getDataRepository().getDataset(request.dataset_id)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.rnaQuantificationsGenerator | def rnaQuantificationsGenerator(self, request):
"""
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"""
if len(request.rna_quantification_set_id) < 1:
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"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.expressionLevelsGenerator | def expressionLevelsGenerator(self, request):
"""
Returns a generator over the (expressionLevel, nextPageToken) pairs
defined by the specified request.
Currently only supports searching over a specified rnaQuantification
"""
rnaQuantificationId = request.rna_quantificati... | python | def expressionLevelsGenerator(self, request):
"""
Returns a generator over the (expressionLevel, nextPageToken) pairs
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Currently only supports searching over a specified rnaQuantification
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetRequest | def runGetRequest(self, obj):
"""
Runs a get request by converting the specified datamodel
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"""
protocolElement = obj.toProtocolElement()
jsonString = protocol.toJson(protocolElement)
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"""
protocolElement = obj.toProtocolElement()
jsonString = protocol.toJson(protocolElement)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchRequest | def runSearchRequest(
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runListReferenceBases | 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 request... | python | def runListReferenceBases(self, requestJson):
"""
Runs a listReferenceBases request for the specified ID and
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetCallSet | 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... | python | 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)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetInfo | def runGetInfo(self, request):
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Returns information about the service including protocol version.
"""
return protocol.toJson(protocol.GetInfoResponse(
protocol_version=protocol.version)) | python | def runGetInfo(self, request):
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Returns information about the service including protocol version.
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runAddAnnouncement | 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.
"""
... | python | def runAddAnnouncement(self, flaskrequest):
"""
Takes a flask request from the frontend and attempts to parse
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runListPeers | def runListPeers(self, request):
"""
Takes a ListPeersRequest and returns a ListPeersResponse using
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"""
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... | python | def runListPeers(self, request):
"""
Takes a ListPeersRequest and returns a ListPeersResponse using
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"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetVariant | def runGetVariant(self, id_):
"""
Returns a variant with the given id
"""
compoundId = datamodel.VariantCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
gaVaria... | python | def runGetVariant(self, id_):
"""
Returns a variant with the given id
"""
compoundId = datamodel.VariantCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetBiosample | def runGetBiosample(self, id_):
"""
Runs a getBiosample request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
biosample = dataset.getBiosample(id_)
return self.r... | python | 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_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetIndividual | 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 se... | python | def runGetIndividual(self, id_):
"""
Runs a getIndividual request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetFeature | 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 =... | python | def runGetFeature(self, id_):
"""
Returns JSON string of the feature object corresponding to
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compoundId = datamodel.FeatureCompoundId.parse(id_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetReadGroupSet | def runGetReadGroupSet(self, id_):
"""
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compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(id_)
return se... | python | def runGetReadGroupSet(self, id_):
"""
Returns a readGroupSet with the given id_
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
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readGroupSet = dataset.getReadGroupSet(id_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetReadGroup | def runGetReadGroup(self, id_):
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dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetReference | 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.getRe... | python | def runGetReference(self, id_):
"""
Runs a getReference request for the specified ID.
"""
compoundId = datamodel.ReferenceCompoundId.parse(id_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetReferenceSet | def runGetReferenceSet(self, id_):
"""
Runs a getReferenceSet request for the specified ID.
"""
referenceSet = self.getDataRepository().getReferenceSet(id_)
return self.runGetRequest(referenceSet) | python | def runGetReferenceSet(self, id_):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetVariantSet | def runGetVariantSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(id_)
return s... | python | def runGetVariantSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantSetCompoundId.parse(id_)
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variantSet = dataset.getVariantSet(id_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetFeatureSet | 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 s... | python | 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_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetContinuousSet | 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_)
... | python | 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_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetDataset | def runGetDataset(self, id_):
"""
Runs a getDataset request for the specified ID.
"""
dataset = self.getDataRepository().getDataset(id_)
return self.runGetRequest(dataset) | python | def runGetDataset(self, id_):
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetVariantAnnotationSet | def runGetVariantAnnotationSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(c... | python | def runGetVariantAnnotationSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
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compoundId = datamodel.VariantAnnotationSetCompoundId.parse(id_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetRnaQuantification | 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.getR... | python | def runGetRnaQuantification(self, id_):
"""
Runs a getRnaQuantification request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationCompoundId.parse(id_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetRnaQuantificationSet | def runGetRnaQuantificationSet(self, id_):
"""
Runs a getRnaQuantificationSet request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_)
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"""
Runs a getRnaQuantificationSet request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetExpressionLevel | def runGetExpressionLevel(self, id_):
"""
Runs a getExpressionLevel request for the specified ID.
"""
compoundId = datamodel.ExpressionLevelCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
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"""
Runs a getExpressionLevel request for the specified ID.
"""
compoundId = datamodel.ExpressionLevelCompoundId.parse(id_)
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchReadGroupSets | def runSearchReadGroupSets(self, request):
"""
Runs the specified SearchReadGroupSetsRequest.
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchIndividuals | def runSearchIndividuals(self, request):
"""
Runs the specified search SearchIndividualsRequest.
"""
return self.runSearchRequest(
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Runs the specified search SearchIndividualsRequest.
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchBiosamples | def runSearchBiosamples(self, request):
"""
Runs the specified SearchBiosamplesRequest.
"""
return self.runSearchRequest(
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Runs the specified SearchBiosamplesRequest.
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchReads | def runSearchReads(self, request):
"""
Runs the specified SearchReadsRequest.
"""
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Runs the specified SearchReadsRequest.
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchReferenceSets | def runSearchReferenceSets(self, request):
"""
Runs the specified SearchReferenceSetsRequest.
"""
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Runs the specified SearchReferenceSetsRequest.
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchReferences | def runSearchReferences(self, request):
"""
Runs the specified SearchReferenceRequest.
"""
return self.runSearchRequest(
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"""
Runs the specified SearchReferenceRequest.
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchVariantSets | def runSearchVariantSets(self, request):
"""
Runs the specified SearchVariantSetsRequest.
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchVariantAnnotationSets | def runSearchVariantAnnotationSets(self, request):
"""
Runs the specified SearchVariantAnnotationSetsRequest.
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchVariants | def runSearchVariants(self, request):
"""
Runs the specified SearchVariantRequest.
"""
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"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchVariantAnnotations | def runSearchVariantAnnotations(self, request):
"""
Runs the specified SearchVariantAnnotationsRequest.
"""
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"""
Runs the specified SearchVariantAnnotationsRequest.
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchCallSets | def runSearchCallSets(self, request):
"""
Runs the specified SearchCallSetsRequest.
"""
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Runs the specified SearchCallSetsRequest.
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchDatasets | def runSearchDatasets(self, request):
"""
Runs the specified SearchDatasetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchDatasetsRequest,
protocol.SearchDatasetsResponse,
self.datasetsGenerator) | python | def runSearchDatasets(self, request):
"""
Runs the specified SearchDatasetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchDatasetsRequest,
protocol.SearchDatasetsResponse,
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchFeatureSets | def runSearchFeatureSets(self, request):
"""
Returns a SearchFeatureSetsResponse for the specified
SearchFeatureSetsRequest object.
"""
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"""
Returns a SearchFeatureSetsResponse for the specified
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchFeatures | 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.runSe... | python | def runSearchFeatures(self, request):
"""
Returns a SearchFeaturesResponse for the specified
SearchFeaturesRequest object.
:param request: JSON string representing searchFeaturesRequest
:return: JSON string representing searchFeatureResponse
"""
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