def searchExpressionLevelsInDb(self,
rnaQuantId,
featureIds=[],
threshold=0.0,
startIndex=0,
maxResults=0):
"""
:param rnaQuantId: string restrict search by quantification id
:param threshold: float minimum expression values to return
:return an array of dictionaries, representing the returned data.
"""
sql = ("SELECT * FROM Expression WHERE "
"rna_quantification_id = ? "
"AND expression > ? ")
sql_args = (rnaQuantId, threshold)
if len(featureIds) > 0:
sql += "AND feature_id in ("
sql += ",".join(['?' for featureId in featureIds])
sql += ") "
for featureId in featureIds:
sql_args += (featureId, )
sql += sqlite_backend.limitsSql(startIndex=startIndex,
maxResults=maxResults)
query = self._dbconn.execute(sql, sql_args)
return sqlite_backend.iterativeFetch(query)
def searchRnaQuantificationsInDb(self, rnaQuantificationId=""):
"""
:param rnaQuantificationId: string restrict search by id
:return an array of dictionaries, representing the returned data.
"""
sql = ("SELECT * FROM RnaQuantification")
sql_args = ()
if len(rnaQuantificationId) > 0:
sql += " WHERE id = ? "
sql_args += (rnaQuantificationId, )
query = self._dbconn.execute(sql, sql_args)
try:
return sqlite_backend.iterativeFetch(query)
except AttributeError:
raise exceptions.RnaQuantificationNotFoundException(
rnaQuantificationId)
def searchRnaQuantificationsInDb(
self, rnaQuantificationId=""):
"""
:param rnaQuantificationId: string restrict search by id
:return an array of dictionaries, representing the returned data.
"""
sql = ("SELECT * FROM RnaQuantification")
sql_args = ()
if len(rnaQuantificationId) > 0:
sql += " WHERE id = ? "
sql_args += (rnaQuantificationId,)
query = self._dbconn.execute(sql, sql_args)
try:
return sqlite_backend.iterativeFetch(query)
except AttributeError:
raise exceptions.RnaQuantificationNotFoundException(
rnaQuantificationId)
def searchExpressionLevelsInDb(
self, rnaQuantId, featureIds=[], threshold=0.0, startIndex=0,
maxResults=0):
"""
:param rnaQuantId: string restrict search by quantification id
:param threshold: float minimum expression values to return
:return an array of dictionaries, representing the returned data.
"""
sql = ("SELECT * FROM Expression WHERE "
"rna_quantification_id = ? "
"AND expression > ? ")
sql_args = (rnaQuantId, threshold)
if len(featureIds) > 0:
sql += "AND feature_id in ("
sql += ",".join(['?' for featureId in featureIds])
sql += ") "
for featureId in featureIds:
sql_args += (featureId,)
sql += sqlite_backend.limitsSql(
startIndex=startIndex, maxResults=maxResults)
query = self._dbconn.execute(sql, sql_args)
return sqlite_backend.iterativeFetch(query)
def iterativeFetchMethod(self):
sql = self._readGroupSql
query = self._dbconn.execute(sql)
iterator = sqlite_backend.iterativeFetch(query, 2)
return iterator
def iterativeFetchMethod(self):
sql = self._readGroupSql
query = self._dbconn.execute(sql)
iterator = sqlite_backend.iterativeFetch(query, 2)
return iterator