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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
the development package.
Assumes a certain directory structure.
"""
path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.append(path) | python | def ga4ghImportGlue():
"""
Call this method before importing a ga4gh module in the scripts dir.
Otherwise, you will be using the installed package instead of
the development package.
Assumes a certain directory structure.
"""
path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.append(path) | [
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | PysamFileHandleCache._update | def _update(self, dataFile, handle):
"""
Update the priority of the file handle. The element is first
removed and then added to the left of the deque.
"""
self._cache.remove((dataFile, handle))
self._add(dataFile, handle) | python | def _update(self, dataFile, handle):
"""
Update the priority of the file handle. The element is first
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"""
self._cache.remove((dataFile, handle))
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | PysamFileHandleCache._removeLru | def _removeLru(self):
"""
Remove the least recently used file handle from the cache.
The pop method removes an element from the right of the deque.
Returns the name of the file that has been removed.
"""
(dataFile, handle) = self._cache.pop()
handle.close()
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"""
Remove the least recently used file handle from the cache.
The pop method removes an element from the right of the deque.
Returns the name of the file that has been removed.
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(dataFile, handle) = self._cache.pop()
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | PysamFileHandleCache.getFileHandle | def getFileHandle(self, dataFile, openMethod):
"""
Returns handle associated to the filename. If the file is
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its handle. Otherwise, open the file using openMethod, store
it in the cache and return the corresponding handle.
"""
if dataFile in self._memoTable:
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self._update(dataFile, handle)
return handle
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try:
handle = openMethod(dataFile)
except ValueError:
raise exceptions.FileOpenFailedException(dataFile)
self._memoTable[dataFile] = handle
self._add(dataFile, handle)
if len(self._memoTable) > self._maxCacheSize:
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del self._memoTable[dataFile]
return handle | python | def getFileHandle(self, dataFile, openMethod):
"""
Returns handle associated to the filename. If the file is
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its handle. Otherwise, open the file using openMethod, store
it in the cache and return the corresponding handle.
"""
if dataFile in self._memoTable:
handle = self._memoTable[dataFile]
self._update(dataFile, handle)
return handle
else:
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handle = openMethod(dataFile)
except ValueError:
raise exceptions.FileOpenFailedException(dataFile)
self._memoTable[dataFile] = handle
self._add(dataFile, handle)
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del self._memoTable[dataFile]
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | CompoundId.join | def join(cls, splits):
"""
Join an array of ids into a compound id string
"""
segments = []
for split in splits:
segments.append('"{}",'.format(split))
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segments[-1] = segments[-1][:-1]
jsonString = '[{}]'.format(''.join(segments))
return jsonString | python | def join(cls, splits):
"""
Join an array of ids into a compound id string
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segments = []
for split in splits:
segments.append('"{}",'.format(split))
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | CompoundId.parse | def parse(cls, compoundIdStr):
"""
Parses the specified compoundId string and returns an instance
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:raises: An ObjectWithIdNotFoundException if parsing fails. This is
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raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
try:
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splits = [cls.decode(split) for split in encodedSplits]
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# pull the differentiator out of the splits before instantiating
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fieldsLength -= 1
if len(splits) != fieldsLength:
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return cls(None, *splits) | python | def parse(cls, compoundIdStr):
"""
Parses the specified compoundId string and returns an instance
of this CompoundId class.
:raises: An ObjectWithIdNotFoundException if parsing fails. This is
because this method is a client-facing method, and if a malformed
identifier (under our internal rules) is provided, the response should
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"""
if not isinstance(compoundIdStr, basestring):
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try:
deobfuscated = cls.deobfuscate(compoundIdStr)
except TypeError:
# When a string that cannot be converted to base64 is passed
# as an argument, b64decode raises a TypeError. We must treat
# this as an ID not found error.
raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
try:
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splits = [cls.decode(split) for split in encodedSplits]
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raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
# pull the differentiator out of the splits before instantiating
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | CompoundId.obfuscate | def obfuscate(cls, idStr):
"""
Mildly obfuscates the specified ID string in an easily reversible
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idStr.encode('utf-8')).replace(b'=', b'')) | python | def obfuscate(cls, idStr):
"""
Mildly obfuscates the specified ID string in an easily reversible
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | CompoundId.deobfuscate | def deobfuscate(cls, data):
"""
Reverses the obfuscation done by the :meth:`obfuscate` method.
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"""
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data + b'A=='[(len(data) - 1) % 4:]))) | python | def deobfuscate(cls, data):
"""
Reverses the obfuscation done by the :meth:`obfuscate` method.
If an identifier arrives without correct base64 padding this
function will append it to the end.
"""
# the str() call is necessary to convert the unicode string
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ga4gh/ga4gh-server | ga4gh/server/datamodel/__init__.py | DatamodelObject.serializeAttributes | def serializeAttributes(self, msg):
"""
Sets the attrbutes of a message during serialization.
"""
attributes = self.getAttributes()
for key in attributes:
protocol.setAttribute(
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return msg | python | def serializeAttributes(self, msg):
"""
Sets the attrbutes of a message during serialization.
"""
attributes = self.getAttributes()
for key in attributes:
protocol.setAttribute(
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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:
scanPath = os.path.join(dataDir, pattern)
for filename in glob.glob(scanPath):
self._addDataFile(filename)
numDataFiles += 1
if numDataFiles == 0:
raise exceptions.EmptyDirException(dataDir, 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
for pattern in patterns:
scanPath = os.path.join(dataDir, pattern)
for filename in glob.glob(scanPath):
self._addDataFile(filename)
numDataFiles += 1
if numDataFiles == 0:
raise exceptions.EmptyDirException(dataDir, patterns) | [
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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://192.168.1.1
The server will attempt to add URLs in this file to its registry at
startup and will log a warning if the file isn't found.
"""
ret = []
with open(filePath) as textFile:
ret = textFile.readlines()
if len(ret) == 0:
if logger:
logger.warn("Couldn't load the initial "
"peer list. Try adding a "
"file named 'initial_peers.txt' "
"to {}".format(os.getcwd()))
# Remove lines that start with a hash or are empty.
return filter(lambda x: x != "" and not x.find("#") != -1, ret) | 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.
# Main ga4gh node
http://1kgenomes.ga4gh.org
# Local intranet peer
https://192.168.1.1
The server will attempt to add URLs in this file to its registry at
startup and will log a warning if the file isn't found.
"""
ret = []
with open(filePath) as textFile:
ret = textFile.readlines()
if len(ret) == 0:
if logger:
logger.warn("Couldn't load the initial "
"peer list. Try adding a "
"file named 'initial_peers.txt' "
"to {}".format(os.getcwd()))
# Remove lines that start with a hash or are empty.
return filter(lambda x: x != "" and not x.find("#") != -1, ret) | [
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# Local intranet peer
https://192.168.1.1
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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 exceptions.RepoManagerException as exc:
if logger:
logger.debug(
"Peer already in registry {} {}".format(peer.getUrl(), exc))
except exceptions.BadUrlException as exc:
if logger:
logger.debug("A URL in the initial "
"peer list {} was malformed. {}".format(url), exc) | python | 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 exceptions.RepoManagerException as exc:
if logger:
logger.debug(
"Peer already in registry {} {}".format(peer.getUrl(), exc))
except exceptions.BadUrlException as exc:
if logger:
logger.debug("A URL in the initial "
"peer list {} was malformed. {}".format(url), exc) | [
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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
for the presence of the URL scheme and netloc using the urlparse
module, and then using a regex.
From http://stackoverflow.com/questions/7160737/
"""
parsed = urlparse.urlparse(urlString)
urlparseValid = parsed.netloc != '' and parsed.scheme != ''
regex = re.compile(
r'^(?:http|ftp)s?://' # http:// or https://
r'(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)'
r'+(?:[A-Z]{2,6}\.?|[A-Z0-9-]{2,}\.?)|' # domain...
r'localhost|' # localhost...
r'\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3})' # ...or ip
r'(?::\d+)?' # optional port
r'(?:/?|[/?]\S+)$', re.IGNORECASE)
return regex.match(urlString) and urlparseValid | python | def isUrl(urlString):
"""
Attempts to return whether a given URL string is valid by checking
for the presence of the URL scheme and netloc using the urlparse
module, and then using a regex.
From http://stackoverflow.com/questions/7160737/
"""
parsed = urlparse.urlparse(urlString)
urlparseValid = parsed.netloc != '' and parsed.scheme != ''
regex = re.compile(
r'^(?:http|ftp)s?://' # http:// or https://
r'(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)'
r'+(?:[A-Z]{2,6}\.?|[A-Z0-9-]{2,}\.?)|' # domain...
r'localhost|' # localhost...
r'\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3})' # ...or ip
r'(?::\d+)?' # optional port
r'(?:/?|[/?]\S+)$', re.IGNORECASE)
return regex.match(urlString) and urlparseValid | [
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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)
return self | [
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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)
return self | [
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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)
return self | [
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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
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_.toProtocolElement(), nextPageToken | python | 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
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_.toProtocolElement(), nextPageToken | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend._protocolObjectGenerator | def _protocolObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, from
a set of protocol objects of the specified size. The objects are
returned by call to the specified method, which must take a single
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currentIndex = 0
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while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_, nextPageToken | python | def _protocolObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, from
a set of protocol objects of the specified size. The objects are
returned by call to the specified method, which must take a single
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"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
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while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
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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
_protocolObjectGenerator to generate page tokens.
"""
return self._protocolObjectGenerator(
request, len(objectList), lambda index: objectList[index]) | python | def _protocolListGenerator(self, request, objectList):
"""
Returns a generator over the objects in the specified list using
_protocolObjectGenerator to generate page tokens.
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend._objectListGenerator | def _objectListGenerator(self, request, objectList):
"""
Returns a generator over the objects in the specified list using
_topLevelObjectGenerator to generate page tokens.
"""
return self._topLevelObjectGenerator(
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"""
Returns a generator over the objects in the specified list using
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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().getDatasetByIndex) | python | 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().getDatasetByIndex) | [
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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._topLevelObjectGenerator(
request, dataset.getNumPhenotypeAssociationSets(),
dataset.getPhenotypeAssociationSetByIndex) | python | 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._topLevelObjectGenerator(
request, dataset.getNumPhenotypeAssociationSets(),
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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(
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dataset.getReadGroupSetByIndex) | 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):
"""
Returns a generator over the results for the specified request, which
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obj = getByIndexMethod(currentIndex)
include = True
rgsp = obj.toProtocolElement()
if request.name and request.name != obj.getLocalId():
include = False
if request.biosample_id and include:
rgsp.ClearField("read_groups")
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if request.biosample_id == readGroup.getBiosampleId():
rgsp.read_groups.extend(
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# If none of the biosamples match and the readgroupset
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if len(rgsp.read_groups) == 0 and \
len(obj.getReadGroups()) != 0:
include = False
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
if include:
yield rgsp, nextPageToken | python | def _readGroupSetsGenerator(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
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currentIndex = 0
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currentIndex, = paging._parsePageToken(
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while currentIndex < numObjects:
obj = getByIndexMethod(currentIndex)
include = True
rgsp = obj.toProtocolElement()
if request.name and request.name != obj.getLocalId():
include = False
if request.biosample_id and include:
rgsp.ClearField("read_groups")
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rgsp.read_groups.extend(
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if len(rgsp.read_groups) == 0 and \
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include = False
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
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yield rgsp, nextPageToken | [
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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
defined by the specified request.
"""
results = []
for obj in self.getDataRepository().getReferenceSets():
include = True
if request.md5checksum:
if request.md5checksum != obj.getMd5Checksum():
include = False
if request.accession:
if request.accession not in obj.getSourceAccessions():
include = False
if request.assembly_id:
if request.assembly_id != obj.getAssemblyId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results) | python | def referenceSetsGenerator(self, request):
"""
Returns a generator over the (referenceSet, nextPageToken) pairs
defined by the specified request.
"""
results = []
for obj in self.getDataRepository().getReferenceSets():
include = True
if request.md5checksum:
if request.md5checksum != obj.getMd5Checksum():
include = False
if request.accession:
if request.accession not in obj.getSourceAccessions():
include = False
if request.assembly_id:
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include = False
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return self._objectListGenerator(request, results) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.referencesGenerator | def referencesGenerator(self, request):
"""
Returns a generator over the (reference, nextPageToken) pairs
defined by the specified request.
"""
referenceSet = self.getDataRepository().getReferenceSet(
request.reference_set_id)
results = []
for obj in referenceSet.getReferences():
include = True
if request.md5checksum:
if request.md5checksum != obj.getMd5Checksum():
include = False
if request.accession:
if request.accession not in obj.getSourceAccessions():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results) | python | def referencesGenerator(self, request):
"""
Returns a generator over the (reference, nextPageToken) pairs
defined by the specified request.
"""
referenceSet = self.getDataRepository().getReferenceSet(
request.reference_set_id)
results = []
for obj in referenceSet.getReferences():
include = True
if request.md5checksum:
if request.md5checksum != obj.getMd5Checksum():
include = False
if request.accession:
if request.accession not in obj.getSourceAccessions():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.variantSetsGenerator | def variantSetsGenerator(self, request):
"""
Returns a generator over the (variantSet, nextPageToken) pairs defined
by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumVariantSets(),
dataset.getVariantSetByIndex) | python | def variantSetsGenerator(self, request):
"""
Returns a generator over the (variantSet, nextPageToken) pairs defined
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"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
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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(
request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(request.variant_set_id)
return self._topLevelObjectGenerator(
request, variantSet.getNumVariantAnnotationSets(),
variantSet.getVariantAnnotationSetByIndex) | python | def variantAnnotationSetsGenerator(self, request):
"""
Returns a generator over the (variantAnnotationSet, nextPageToken)
pairs defined by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(request.variant_set_id)
return self._topLevelObjectGenerator(
request, variantSet.getNumVariantAnnotationSets(),
variantSet.getVariantAnnotationSetByIndex) | [
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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
by the specified request
"""
if not request.reference_id:
raise exceptions.UnmappedReadsNotSupported()
if len(request.read_group_ids) < 1:
raise exceptions.BadRequestException(
"At least one readGroupId must be specified")
elif len(request.read_group_ids) == 1:
return self._readsGeneratorSingle(request)
else:
return self._readsGeneratorMultiple(request) | python | def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
by the specified request
"""
if not request.reference_id:
raise exceptions.UnmappedReadsNotSupported()
if len(request.read_group_ids) < 1:
raise exceptions.BadRequestException(
"At least one readGroupId must be specified")
elif len(request.read_group_ids) == 1:
return self._readsGeneratorSingle(request)
else:
return self._readsGeneratorMultiple(request) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.variantsGenerator | def variantsGenerator(self, request):
"""
Returns a generator over the (variant, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId \
.parse(request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
intervalIterator = paging.VariantsIntervalIterator(
request, variantSet)
return intervalIterator | python | def variantsGenerator(self, request):
"""
Returns a generator over the (variant, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId \
.parse(request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
intervalIterator = paging.VariantsIntervalIterator(
request, variantSet)
return intervalIterator | [
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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(
request.variant_annotation_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
variantAnnotationSet = variantSet.getVariantAnnotationSet(
request.variant_annotation_set_id)
iterator = paging.VariantAnnotationsIntervalIterator(
request, variantAnnotationSet)
return iterator | python | def variantAnnotationsGenerator(self, request):
"""
Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
defined by the specified request.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(
request.variant_annotation_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
variantAnnotationSet = variantSet.getVariantAnnotationSet(
request.variant_annotation_set_id)
iterator = paging.VariantAnnotationsIntervalIterator(
request, variantAnnotationSet)
return iterator | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.featuresGenerator | def featuresGenerator(self, request):
"""
Returns a generator over the (features, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
parentId = None
if request.feature_set_id != "":
compoundId = datamodel.FeatureSetCompoundId.parse(
request.feature_set_id)
if request.parent_id != "":
compoundParentId = datamodel.FeatureCompoundId.parse(
request.parent_id)
parentId = compoundParentId.featureId
# A client can optionally specify JUST the (compound) parentID,
# and the server needs to derive the dataset & featureSet
# from this (compound) parentID.
if compoundId is None:
compoundId = compoundParentId
else:
# check that the dataset and featureSet of the parent
# compound ID is the same as that of the featureSetId
mismatchCheck = (
compoundParentId.dataset_id != compoundId.dataset_id or
compoundParentId.feature_set_id !=
compoundId.feature_set_id)
if mismatchCheck:
raise exceptions.ParentIncompatibleWithFeatureSet()
if compoundId is None:
raise exceptions.FeatureSetNotSpecifiedException()
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
featureSet = dataset.getFeatureSet(compoundId.feature_set_id)
iterator = paging.FeaturesIterator(
request, featureSet, parentId)
return iterator | python | def featuresGenerator(self, request):
"""
Returns a generator over the (features, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
parentId = None
if request.feature_set_id != "":
compoundId = datamodel.FeatureSetCompoundId.parse(
request.feature_set_id)
if request.parent_id != "":
compoundParentId = datamodel.FeatureCompoundId.parse(
request.parent_id)
parentId = compoundParentId.featureId
# A client can optionally specify JUST the (compound) parentID,
# and the server needs to derive the dataset & featureSet
# from this (compound) parentID.
if compoundId is None:
compoundId = compoundParentId
else:
# check that the dataset and featureSet of the parent
# compound ID is the same as that of the featureSetId
mismatchCheck = (
compoundParentId.dataset_id != compoundId.dataset_id or
compoundParentId.feature_set_id !=
compoundId.feature_set_id)
if mismatchCheck:
raise exceptions.ParentIncompatibleWithFeatureSet()
if compoundId is None:
raise exceptions.FeatureSetNotSpecifiedException()
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
featureSet = dataset.getFeatureSet(compoundId.feature_set_id)
iterator = paging.FeaturesIterator(
request, featureSet, parentId)
return iterator | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.continuousGenerator | def continuousGenerator(self, request):
"""
Returns a generator over the (continuous, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
if request.continuous_set_id != "":
compoundId = datamodel.ContinuousSetCompoundId.parse(
request.continuous_set_id)
if compoundId is None:
raise exceptions.ContinuousSetNotSpecifiedException()
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
continuousSet = dataset.getContinuousSet(request.continuous_set_id)
iterator = paging.ContinuousIterator(request, continuousSet)
return iterator | python | def continuousGenerator(self, request):
"""
Returns a generator over the (continuous, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
if request.continuous_set_id != "":
compoundId = datamodel.ContinuousSetCompoundId.parse(
request.continuous_set_id)
if compoundId is None:
raise exceptions.ContinuousSetNotSpecifiedException()
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
continuousSet = dataset.getContinuousSet(request.continuous_set_id)
iterator = paging.ContinuousIterator(request, continuousSet)
return iterator | [
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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(
request.phenotype_association_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSet(
compoundId.phenotypeAssociationSetId)
associations = phenotypeAssociationSet.getAssociations(request)
phenotypes = [association.phenotype for association in associations]
return self._protocolListGenerator(
request, phenotypes) | python | 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(
request.phenotype_association_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSet(
compoundId.phenotypeAssociationSetId)
associations = phenotypeAssociationSet.getAssociations(request)
phenotypes = [association.phenotype for association in associations]
return self._protocolListGenerator(
request, phenotypes) | [
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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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dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSet(
compoundId.phenotypeAssociationSetId)
featureSets = dataset.getFeatureSets()
annotationList = phenotypeAssociationSet.getAssociations(
request, featureSets)
return self._protocolListGenerator(request, annotationList) | python | 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(
request.phenotype_association_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSet(
compoundId.phenotypeAssociationSetId)
featureSets = dataset.getFeatureSets()
annotationList = phenotypeAssociationSet.getAssociations(
request, featureSets)
return self._protocolListGenerator(request, annotationList) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.callSetsGenerator | def callSetsGenerator(self, request):
"""
Returns a generator over the (callSet, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
results = []
for obj in variantSet.getCallSets():
include = True
if request.name:
if request.name != obj.getLocalId():
include = False
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results) | python | def callSetsGenerator(self, request):
"""
Returns a generator over the (callSet, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
results = []
for obj in variantSet.getCallSets():
include = True
if request.name:
if request.name != obj.getLocalId():
include = False
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.featureSetsGenerator | def featureSetsGenerator(self, request):
"""
Returns a generator over the (featureSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumFeatureSets(),
dataset.getFeatureSetByIndex) | python | def featureSetsGenerator(self, request):
"""
Returns a generator over the (featureSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumFeatureSets(),
dataset.getFeatureSetByIndex) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.continuousSetsGenerator | def continuousSetsGenerator(self, request):
"""
Returns a generator over the (continuousSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumContinuousSets(),
dataset.getContinuousSetByIndex) | python | def continuousSetsGenerator(self, request):
"""
Returns a generator over the (continuousSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumContinuousSets(),
dataset.getContinuousSetByIndex) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.rnaQuantificationSetsGenerator | def rnaQuantificationSetsGenerator(self, request):
"""
Returns a generator over the (rnaQuantificationSet, nextPageToken)
pairs defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumRnaQuantificationSets(),
dataset.getRnaQuantificationSetByIndex) | python | def rnaQuantificationSetsGenerator(self, request):
"""
Returns a generator over the (rnaQuantificationSet, nextPageToken)
pairs defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumRnaQuantificationSets(),
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.rnaQuantificationsGenerator | def rnaQuantificationsGenerator(self, request):
"""
Returns a generator over the (rnaQuantification, nextPageToken) pairs
defined by the specified request.
"""
if len(request.rna_quantification_set_id) < 1:
raise exceptions.BadRequestException(
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else:
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(
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dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
results = []
for obj in rnaQuantSet.getRnaQuantifications():
include = True
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results) | python | def rnaQuantificationsGenerator(self, request):
"""
Returns a generator over the (rnaQuantification, nextPageToken) pairs
defined by the specified request.
"""
if len(request.rna_quantification_set_id) < 1:
raise exceptions.BadRequestException(
"Rna Quantification Set Id must be specified")
else:
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(
request.rna_quantification_set_id)
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
results = []
for obj in rnaQuantSet.getRnaQuantifications():
include = True
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results) | [
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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_quantification_id
compoundId = datamodel.RnaQuantificationCompoundId.parse(
request.rna_quantification_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuant = rnaQuantSet.getRnaQuantification(rnaQuantificationId)
rnaQuantificationId = rnaQuant.getLocalId()
iterator = paging.ExpressionLevelsIterator(
request, rnaQuant)
return iterator | python | 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_quantification_id
compoundId = datamodel.RnaQuantificationCompoundId.parse(
request.rna_quantification_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuant = rnaQuantSet.getRnaQuantification(rnaQuantificationId)
rnaQuantificationId = rnaQuant.getLocalId()
iterator = paging.ExpressionLevelsIterator(
request, rnaQuant)
return iterator | [
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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
object into its protocol representation.
"""
protocolElement = obj.toProtocolElement()
jsonString = protocol.toJson(protocolElement)
return jsonString | python | def runGetRequest(self, obj):
"""
Runs a get request by converting the specified datamodel
object into its protocol representation.
"""
protocolElement = obj.toProtocolElement()
jsonString = protocol.toJson(protocolElement)
return jsonString | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchRequest | def runSearchRequest(
self, requestStr, requestClass, responseClass, objectGenerator):
"""
Runs the specified request. The request is a string containing
a JSON representation of an instance of the specified requestClass.
We return a string representation of an instance of the specified
responseClass in JSON format. Objects are filled into the page list
using the specified object generator, which must return
(object, nextPageToken) pairs, and be able to resume iteration from
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"""
self.startProfile()
try:
request = protocol.fromJson(requestStr, requestClass)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestStr)
# TODO How do we detect when the page size is not set?
if not request.page_size:
request.page_size = self._defaultPageSize
if request.page_size < 0:
raise exceptions.BadPageSizeException(request.page_size)
responseBuilder = response_builder.SearchResponseBuilder(
responseClass, request.page_size, self._maxResponseLength)
nextPageToken = None
for obj, nextPageToken in objectGenerator(request):
responseBuilder.addValue(obj)
if responseBuilder.isFull():
break
responseBuilder.setNextPageToken(nextPageToken)
responseString = responseBuilder.getSerializedResponse()
self.endProfile()
return responseString | python | def runSearchRequest(
self, requestStr, requestClass, responseClass, objectGenerator):
"""
Runs the specified request. The request is a string containing
a JSON representation of an instance of the specified requestClass.
We return a string representation of an instance of the specified
responseClass in JSON format. Objects are filled into the page list
using the specified object generator, which must return
(object, nextPageToken) pairs, and be able to resume iteration from
any point using the nextPageToken attribute of the request object.
"""
self.startProfile()
try:
request = protocol.fromJson(requestStr, requestClass)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestStr)
# TODO How do we detect when the page size is not set?
if not request.page_size:
request.page_size = self._defaultPageSize
if request.page_size < 0:
raise exceptions.BadPageSizeException(request.page_size)
responseBuilder = response_builder.SearchResponseBuilder(
responseClass, request.page_size, self._maxResponseLength)
nextPageToken = None
for obj, nextPageToken in objectGenerator(request):
responseBuilder.addValue(obj)
if responseBuilder.isFull():
break
responseBuilder.setNextPageToken(nextPageToken)
responseString = responseBuilder.getSerializedResponse()
self.endProfile()
return responseString | [
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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 requestJson:
request = protocol.ListReferenceBasesRequest()
else:
try:
request = protocol.fromJson(
requestJson,
protocol.ListReferenceBasesRequest)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestJson)
compoundId = datamodel.ReferenceCompoundId.parse(request.reference_id)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(request.reference_id)
start = request.start
end = request.end
if end == 0: # assume meant "get all"
end = reference.getLength()
if request.page_token:
pageTokenStr = request.page_token
start = paging._parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
nextPageToken = None
if start + chunkSize < end:
end = start + chunkSize
nextPageToken = str(start + chunkSize)
sequence = reference.getBases(start, end)
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
if nextPageToken:
response.next_page_token = nextPageToken
return protocol.toJson(response) | python | def runListReferenceBases(self, requestJson):
"""
Runs a listReferenceBases request for the specified ID and
request arguments.
"""
# In the case when an empty post request is made to the endpoint
# we instantiate an empty ListReferenceBasesRequest.
if not requestJson:
request = protocol.ListReferenceBasesRequest()
else:
try:
request = protocol.fromJson(
requestJson,
protocol.ListReferenceBasesRequest)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestJson)
compoundId = datamodel.ReferenceCompoundId.parse(request.reference_id)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(request.reference_id)
start = request.start
end = request.end
if end == 0: # assume meant "get all"
end = reference.getLength()
if request.page_token:
pageTokenStr = request.page_token
start = paging._parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
nextPageToken = None
if start + chunkSize < end:
end = start + chunkSize
nextPageToken = str(start + chunkSize)
sequence = reference.getBases(start, end)
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
if nextPageToken:
response.next_page_token = nextPageToken
return protocol.toJson(response) | [
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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 = variantSet.getCallSet(id_)
return self.runGetRequest(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)
callSet = variantSet.getCallSet(id_)
return self.runGetRequest(callSet) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetInfo | def runGetInfo(self, request):
"""
Returns information about the service including protocol version.
"""
return protocol.toJson(protocol.GetInfoResponse(
protocol_version=protocol.version)) | python | def runGetInfo(self, request):
"""
Returns information about the service including protocol version.
"""
return protocol.toJson(protocol.GetInfoResponse(
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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.
"""
announcement = {}
# We want to parse the request ourselves to collect a little more
# data about it.
try:
requestData = protocol.fromJson(
flaskrequest.get_data(), protocol.AnnouncePeerRequest)
announcement['hostname'] = flaskrequest.host_url
announcement['remote_addr'] = flaskrequest.remote_addr
announcement['user_agent'] = flaskrequest.headers.get('User-Agent')
except AttributeError:
# Sometimes in testing we will send protocol requests instead
# of flask requests and so the hostname and user agent won't
# be present.
try:
requestData = protocol.fromJson(
flaskrequest, protocol.AnnouncePeerRequest)
except Exception as e:
raise exceptions.InvalidJsonException(e)
except Exception as e:
raise exceptions.InvalidJsonException(e)
# Validate the url before accepting the announcement
peer = datamodel.peers.Peer(requestData.peer.url)
peer.setAttributesJson(protocol.toJson(
requestData.peer.attributes))
announcement['url'] = peer.getUrl()
announcement['attributes'] = peer.getAttributes()
try:
self.getDataRepository().insertAnnouncement(announcement)
except:
raise exceptions.BadRequestException(announcement['url'])
return protocol.toJson(
protocol.AnnouncePeerResponse(success=True)) | python | def runAddAnnouncement(self, flaskrequest):
"""
Takes a flask request from the frontend and attempts to parse
into an AnnouncePeerRequest. If successful, it will log the
announcement to the `announcement` table with some other metadata
gathered from the request.
"""
announcement = {}
# We want to parse the request ourselves to collect a little more
# data about it.
try:
requestData = protocol.fromJson(
flaskrequest.get_data(), protocol.AnnouncePeerRequest)
announcement['hostname'] = flaskrequest.host_url
announcement['remote_addr'] = flaskrequest.remote_addr
announcement['user_agent'] = flaskrequest.headers.get('User-Agent')
except AttributeError:
# Sometimes in testing we will send protocol requests instead
# of flask requests and so the hostname and user agent won't
# be present.
try:
requestData = protocol.fromJson(
flaskrequest, protocol.AnnouncePeerRequest)
except Exception as e:
raise exceptions.InvalidJsonException(e)
except Exception as e:
raise exceptions.InvalidJsonException(e)
# Validate the url before accepting the announcement
peer = datamodel.peers.Peer(requestData.peer.url)
peer.setAttributesJson(protocol.toJson(
requestData.peer.attributes))
announcement['url'] = peer.getUrl()
announcement['attributes'] = peer.getAttributes()
try:
self.getDataRepository().insertAnnouncement(announcement)
except:
raise exceptions.BadRequestException(announcement['url'])
return protocol.toJson(
protocol.AnnouncePeerResponse(success=True)) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runListPeers | def runListPeers(self, request):
"""
Takes a ListPeersRequest and returns a ListPeersResponse using
a page_token and page_size if provided.
"""
return self.runSearchRequest(
request,
protocol.ListPeersRequest,
protocol.ListPeersResponse,
self.peersGenerator) | python | def runListPeers(self, request):
"""
Takes a ListPeersRequest and returns a ListPeersResponse using
a page_token and page_size if provided.
"""
return self.runSearchRequest(
request,
protocol.ListPeersRequest,
protocol.ListPeersResponse,
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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)
gaVariant = variantSet.getVariant(compoundId)
# TODO variant is a special case here, as it's returning a
# protocol element rather than a datamodel object. We should
# fix this for consistency.
jsonString = protocol.toJson(gaVariant)
return jsonString | 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)
gaVariant = variantSet.getVariant(compoundId)
# TODO variant is a special case here, as it's returning a
# protocol element rather than a datamodel object. We should
# fix this for consistency.
jsonString = protocol.toJson(gaVariant)
return jsonString | [
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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.runGetRequest(biosample) | 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_)
return self.runGetRequest(biosample) | [
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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 self.runGetRequest(individual) | python | 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_)
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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 = dataset.getFeatureSet(compoundId.feature_set_id)
gaFeature = featureSet.getFeature(compoundId)
jsonString = protocol.toJson(gaFeature)
return jsonString | python | def runGetFeature(self, id_):
"""
Returns JSON string of the feature object corresponding to
the feature compoundID passed in.
"""
compoundId = datamodel.FeatureCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
featureSet = dataset.getFeatureSet(compoundId.feature_set_id)
gaFeature = featureSet.getFeature(compoundId)
jsonString = protocol.toJson(gaFeature)
return jsonString | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetReadGroupSet | def runGetReadGroupSet(self, id_):
"""
Returns a readGroupSet with the given id_
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(id_)
return self.runGetRequest(readGroupSet) | python | def runGetReadGroupSet(self, id_):
"""
Returns a readGroupSet with the given id_
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(id_)
return self.runGetRequest(readGroupSet) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runGetReadGroup | def runGetReadGroup(self, id_):
"""
Returns a read group with the given id_
"""
compoundId = datamodel.ReadGroupCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
readGroup = readGroupSet.getReadGroup(id_)
return self.runGetRequest(readGroup) | python | def runGetReadGroup(self, id_):
"""
Returns a read group with the given id_
"""
compoundId = datamodel.ReadGroupCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
readGroup = readGroupSet.getReadGroup(id_)
return self.runGetRequest(readGroup) | [
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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(
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reference = referenceSet.getReference(id_)
return self.runGetRequest(reference) | python | def runGetReference(self, id_):
"""
Runs a getReference request for the specified ID.
"""
compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(id_)
return self.runGetRequest(reference) | [
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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_):
"""
Runs a getReferenceSet request for the specified ID.
"""
referenceSet = self.getDataRepository().getReferenceSet(id_)
return self.runGetRequest(referenceSet) | [
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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 self.runGetRequest(variantSet) | python | 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 self.runGetRequest(variantSet) | [
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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 self.runGetRequest(featureSet) | 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_)
return self.runGetRequest(featureSet) | [
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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_)
return self.runGetRequest(continuousSet) | 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_)
return self.runGetRequest(continuousSet) | [
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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_):
"""
Runs a getDataset request for the specified ID.
"""
dataset = self.getDataRepository().getDataset(id_)
return self.runGetRequest(dataset) | [
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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(compoundId.variant_set_id)
variantAnnotationSet = variantSet.getVariantAnnotationSet(id_)
return self.runGetRequest(variantAnnotationSet) | python | 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(compoundId.variant_set_id)
variantAnnotationSet = variantSet.getVariantAnnotationSet(id_)
return self.runGetRequest(variantAnnotationSet) | [
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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.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(id_)
return self.runGetRequest(rnaQuantification) | python | def runGetRnaQuantification(self, id_):
"""
Runs a getRnaQuantification request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(id_)
return self.runGetRequest(rnaQuantification) | [
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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_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(id_)
return self.runGetRequest(rnaQuantificationSet) | python | def runGetRnaQuantificationSet(self, id_):
"""
Runs a getRnaQuantificationSet request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(id_)
return self.runGetRequest(rnaQuantificationSet) | [
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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)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
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rnaQuantification = rnaQuantificationSet.getRnaQuantification(
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expressionLevel = rnaQuantification.getExpressionLevel(compoundId)
return self.runGetRequest(expressionLevel) | python | def runGetExpressionLevel(self, id_):
"""
Runs a getExpressionLevel request for the specified ID.
"""
compoundId = datamodel.ExpressionLevelCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(
compoundId.rna_quantification_id)
expressionLevel = rnaQuantification.getExpressionLevel(compoundId)
return self.runGetRequest(expressionLevel) | [
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchReadGroupSets | def runSearchReadGroupSets(self, request):
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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(
request, protocol.SearchIndividualsRequest,
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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):
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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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return self.runSearchRequest(
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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.
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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):
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchVariantAnnotationSets | def runSearchVariantAnnotationSets(self, request):
"""
Runs the specified SearchVariantAnnotationSetsRequest.
"""
return self.runSearchRequest(
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchVariants | def runSearchVariants(self, request):
"""
Runs the specified SearchVariantRequest.
"""
return self.runSearchRequest(
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Runs the specified SearchVariantRequest.
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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.
"""
return self.runSearchRequest(
request, protocol.SearchCallSetsRequest,
protocol.SearchCallSetsResponse,
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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,
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"""
Runs the specified SearchDatasetsRequest.
"""
return self.runSearchRequest(
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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.
"""
return self.runSearchRequest(
request, protocol.SearchFeatureSetsRequest,
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"""
Returns a SearchFeatureSetsResponse for the specified
SearchFeatureSetsRequest object.
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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.runSearchRequest(
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"""
Returns a SearchFeaturesResponse for the specified
SearchFeaturesRequest object.
:param request: JSON string representing searchFeaturesRequest
:return: JSON string representing searchFeatureResponse
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchContinuousSets | def runSearchContinuousSets(self, request):
"""
Returns a SearchContinuousSetsResponse for the specified
SearchContinuousSetsRequest object.
"""
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchContinuous | def runSearchContinuous(self, request):
"""
Returns a SearchContinuousResponse for the specified
SearchContinuousRequest object.
:param request: JSON string representing searchContinuousRequest
:return: JSON string representing searchContinuousResponse
"""
return self.runSearchRequest(
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"""
Returns a SearchContinuousResponse for the specified
SearchContinuousRequest object.
:param request: JSON string representing searchContinuousRequest
:return: JSON string representing searchContinuousResponse
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchRnaQuantificationSets | def runSearchRnaQuantificationSets(self, request):
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SearchRnaQuantificationSetsRequest object.
"""
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"""
Returns a SearchRnaQuantificationSetsResponse for the specified
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchRnaQuantifications | def runSearchRnaQuantifications(self, request):
"""
Returns a SearchRnaQuantificationResponse for the specified
SearchRnaQuantificationRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchRnaQuantificationsRequest,
protocol.SearchRnaQuantificationsResponse,
self.rnaQuantificationsGenerator) | python | def runSearchRnaQuantifications(self, request):
"""
Returns a SearchRnaQuantificationResponse for the specified
SearchRnaQuantificationRequest object.
"""
return self.runSearchRequest(
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ga4gh/ga4gh-server | ga4gh/server/backend.py | Backend.runSearchExpressionLevels | def runSearchExpressionLevels(self, request):
"""
Returns a SearchExpressionLevelResponse for the specified
SearchExpressionLevelRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchExpressionLevelsRequest,
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"""
Returns a SearchExpressionLevelResponse for the specified
SearchExpressionLevelRequest object.
"""
return self.runSearchRequest(
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.populateFromRow | def populateFromRow(self, dataset):
"""
Populates the instance variables of this Dataset from the
specified database row.
"""
self._description = dataset.description
self.setAttributesJson(dataset.attributes) | python | def populateFromRow(self, dataset):
"""
Populates the instance variables of this Dataset from the
specified database row.
"""
self._description = dataset.description
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.addVariantSet | def addVariantSet(self, variantSet):
"""
Adds the specified variantSet to this dataset.
"""
id_ = variantSet.getId()
self._variantSetIdMap[id_] = variantSet
self._variantSetNameMap[variantSet.getLocalId()] = variantSet
self._variantSetIds.append(id_) | python | def addVariantSet(self, variantSet):
"""
Adds the specified variantSet to this dataset.
"""
id_ = variantSet.getId()
self._variantSetIdMap[id_] = variantSet
self._variantSetNameMap[variantSet.getLocalId()] = variantSet
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.addBiosample | def addBiosample(self, biosample):
"""
Adds the specified biosample to this dataset.
"""
id_ = biosample.getId()
self._biosampleIdMap[id_] = biosample
self._biosampleIds.append(id_)
self._biosampleNameMap[biosample.getName()] = biosample | python | def addBiosample(self, biosample):
"""
Adds the specified biosample to this dataset.
"""
id_ = biosample.getId()
self._biosampleIdMap[id_] = biosample
self._biosampleIds.append(id_)
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.addIndividual | def addIndividual(self, individual):
"""
Adds the specified individual to this dataset.
"""
id_ = individual.getId()
self._individualIdMap[id_] = individual
self._individualIds.append(id_)
self._individualNameMap[individual.getName()] = individual | python | def addIndividual(self, individual):
"""
Adds the specified individual to this dataset.
"""
id_ = individual.getId()
self._individualIdMap[id_] = individual
self._individualIds.append(id_)
self._individualNameMap[individual.getName()] = individual | [
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.addFeatureSet | def addFeatureSet(self, featureSet):
"""
Adds the specified featureSet to this dataset.
"""
id_ = featureSet.getId()
self._featureSetIdMap[id_] = featureSet
self._featureSetIds.append(id_)
name = featureSet.getLocalId()
self._featureSetNameMap[name] = featureSet | python | def addFeatureSet(self, featureSet):
"""
Adds the specified featureSet to this dataset.
"""
id_ = featureSet.getId()
self._featureSetIdMap[id_] = featureSet
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.addContinuousSet | def addContinuousSet(self, continuousSet):
"""
Adds the specified continuousSet to this dataset.
"""
id_ = continuousSet.getId()
self._continuousSetIdMap[id_] = continuousSet
self._continuousSetIds.append(id_)
name = continuousSet.getLocalId()
self._continuousSetNameMap[name] = continuousSet | python | def addContinuousSet(self, continuousSet):
"""
Adds the specified continuousSet to this dataset.
"""
id_ = continuousSet.getId()
self._continuousSetIdMap[id_] = continuousSet
self._continuousSetIds.append(id_)
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.addReadGroupSet | def addReadGroupSet(self, readGroupSet):
"""
Adds the specified readGroupSet to this dataset.
"""
id_ = readGroupSet.getId()
self._readGroupSetIdMap[id_] = readGroupSet
self._readGroupSetNameMap[readGroupSet.getLocalId()] = readGroupSet
self._readGroupSetIds.append(id_) | python | def addReadGroupSet(self, readGroupSet):
"""
Adds the specified readGroupSet to this dataset.
"""
id_ = readGroupSet.getId()
self._readGroupSetIdMap[id_] = readGroupSet
self._readGroupSetNameMap[readGroupSet.getLocalId()] = readGroupSet
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.addRnaQuantificationSet | def addRnaQuantificationSet(self, rnaQuantSet):
"""
Adds the specified rnaQuantification set to this dataset.
"""
id_ = rnaQuantSet.getId()
self._rnaQuantificationSetIdMap[id_] = rnaQuantSet
self._rnaQuantificationSetIds.append(id_)
name = rnaQuantSet.getLocalId()
self._rnaQuantificationSetNameMap[name] = rnaQuantSet | python | def addRnaQuantificationSet(self, rnaQuantSet):
"""
Adds the specified rnaQuantification set to this dataset.
"""
id_ = rnaQuantSet.getId()
self._rnaQuantificationSetIdMap[id_] = rnaQuantSet
self._rnaQuantificationSetIds.append(id_)
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.getVariantSet | def getVariantSet(self, id_):
"""
Returns the VariantSet with the specified name, or raises a
VariantSetNotFoundException otherwise.
"""
if id_ not in self._variantSetIdMap:
raise exceptions.VariantSetNotFoundException(id_)
return self._variantSetIdMap[id_] | python | def getVariantSet(self, id_):
"""
Returns the VariantSet with the specified name, or raises a
VariantSetNotFoundException otherwise.
"""
if id_ not in self._variantSetIdMap:
raise exceptions.VariantSetNotFoundException(id_)
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.getVariantSetByName | def getVariantSetByName(self, name):
"""
Returns a VariantSet with the specified name, or raises a
VariantSetNameNotFoundException if it does not exist.
"""
if name not in self._variantSetNameMap:
raise exceptions.VariantSetNameNotFoundException(name)
return self._variantSetNameMap[name] | python | def getVariantSetByName(self, name):
"""
Returns a VariantSet with the specified name, or raises a
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"""
if name not in self._variantSetNameMap:
raise exceptions.VariantSetNameNotFoundException(name)
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.addPhenotypeAssociationSet | def addPhenotypeAssociationSet(self, phenotypeAssociationSet):
"""
Adds the specified g2p association set to this backend.
"""
id_ = phenotypeAssociationSet.getId()
self._phenotypeAssociationSetIdMap[id_] = phenotypeAssociationSet
self._phenotypeAssociationSetNameMap[
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self._phenotypeAssociationSetIds.append(id_) | python | def addPhenotypeAssociationSet(self, phenotypeAssociationSet):
"""
Adds the specified g2p association set to this backend.
"""
id_ = phenotypeAssociationSet.getId()
self._phenotypeAssociationSetIdMap[id_] = phenotypeAssociationSet
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.getFeatureSet | def getFeatureSet(self, id_):
"""
Returns the FeatureSet with the specified id, or raises a
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"""
if id_ not in self._featureSetIdMap:
raise exceptions.FeatureSetNotFoundException(id_)
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"""
Returns the FeatureSet with the specified id, or raises a
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] | 1aa18922ef136db8604f6f098cb1732cba6f2a76 | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/datasets.py#L224-L231 | train |
ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.getFeatureSetByName | def getFeatureSetByName(self, name):
"""
Returns the FeatureSet with the specified name, or raises
an exception otherwise.
"""
if name not in self._featureSetNameMap:
raise exceptions.FeatureSetNameNotFoundException(name)
return self._featureSetNameMap[name] | python | def getFeatureSetByName(self, name):
"""
Returns the FeatureSet with the specified name, or raises
an exception otherwise.
"""
if name not in self._featureSetNameMap:
raise exceptions.FeatureSetNameNotFoundException(name)
return self._featureSetNameMap[name] | [
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.getContinuousSet | def getContinuousSet(self, id_):
"""
Returns the ContinuousSet with the specified id, or raises a
ContinuousSetNotFoundException otherwise.
"""
if id_ not in self._continuousSetIdMap:
raise exceptions.ContinuousSetNotFoundException(id_)
return self._continuousSetIdMap[id_] | python | def getContinuousSet(self, id_):
"""
Returns the ContinuousSet with the specified id, or raises a
ContinuousSetNotFoundException otherwise.
"""
if id_ not in self._continuousSetIdMap:
raise exceptions.ContinuousSetNotFoundException(id_)
return self._continuousSetIdMap[id_] | [
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.getContinuousSetByName | def getContinuousSetByName(self, name):
"""
Returns the ContinuousSet with the specified name, or raises
an exception otherwise.
"""
if name not in self._continuousSetNameMap:
raise exceptions.ContinuousSetNameNotFoundException(name)
return self._continuousSetNameMap[name] | python | def getContinuousSetByName(self, name):
"""
Returns the ContinuousSet with the specified name, or raises
an exception otherwise.
"""
if name not in self._continuousSetNameMap:
raise exceptions.ContinuousSetNameNotFoundException(name)
return self._continuousSetNameMap[name] | [
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.getBiosampleByName | def getBiosampleByName(self, name):
"""
Returns a Biosample with the specified name, or raises a
BiosampleNameNotFoundException if it does not exist.
"""
if name not in self._biosampleNameMap:
raise exceptions.BiosampleNameNotFoundException(name)
return self._biosampleNameMap[name] | python | def getBiosampleByName(self, name):
"""
Returns a Biosample with the specified name, or raises a
BiosampleNameNotFoundException if it does not exist.
"""
if name not in self._biosampleNameMap:
raise exceptions.BiosampleNameNotFoundException(name)
return self._biosampleNameMap[name] | [
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ga4gh/ga4gh-server | ga4gh/server/datamodel/datasets.py | Dataset.getBiosample | def getBiosample(self, id_):
"""
Returns the Biosample with the specified id, or raises
a BiosampleNotFoundException otherwise.
"""
if id_ not in self._biosampleIdMap:
raise exceptions.BiosampleNotFoundException(id_)
return self._biosampleIdMap[id_] | python | def getBiosample(self, id_):
"""
Returns the Biosample with the specified id, or raises
a BiosampleNotFoundException otherwise.
"""
if id_ not in self._biosampleIdMap:
raise exceptions.BiosampleNotFoundException(id_)
return self._biosampleIdMap[id_] | [
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