def simpleUpdateWrapper(self, valueDict, db, genome, column):
"""
If your classifier is going to do a simple 1-1 update with a valueDict, use this.
"""
with sql_lib.ExclusiveSqlConnection(db) as cur:
sql_lib.updateRows(cur, genome, self.primaryKeyColumn, column,
self.invertDict(valueDict))
def simpleBedUpdateWrapper(self, valueDict, db, genome, column):
"""
If your details-mode classifier has BED records for values in its valueDict, use this.
"""
with sql_lib.ExclusiveSqlConnection(db) as cur:
sql_lib.updateRows(cur, genome, self.primaryKeyColumn, column,
self.detailsEntryIter(valueDict.iteritems()))
def initializeSqlTable(self, db, genome, columns, primaryKey):
with sql_lib.ExclusiveSqlConnection(db) as cur:
sql_lib.initializeTable(cur,
genome,
columns,
primaryKey,
drop_if_exists=True)
def upsert_dict_wrapper(self, d):
"""even more convenient wrapper for upserting. Assumes input is a dict
mapping alignment names to a value.
"""
with sql_lib.ExclusiveSqlConnection(self.db) as cur:
for aln, value in d.iteritems():
sql_lib.upsert(cur, self.genome, self.primary_key, aln,
self.__class__.__name__, str(value))
def buildNameRow(self, db, genome, aug_aIds, aIds, primaryKey):
with sql_lib.ExclusiveSqlConnection(db) as cur:
cur.execute(
"""ALTER TABLE '{}' ADD COLUMN aId TEXT """.format(genome))
sql_lib.updateRows(cur, genome, primaryKey, "aId",
izip(aIds, aug_aIds))
def initializeSqlRows(self, db, genome, aIds, primaryKey):
with sql_lib.ExclusiveSqlConnection(db) as cur:
sql_lib.insertRows(cur, genome, primaryKey, [primaryKey],
izip_longest(aIds, [None]))
def upsert_wrapper(self, alignmentName, value):
"""convenience wrapper for upserting into a column in the sql lib.
So you don't have to call __name__, self.primaryKey, etc each time"""
with sql_lib.ExclusiveSqlConnection(self.db) as cur:
sql_lib.upsert(cur, self.genome, self.primary_key, alignmentName,
self.__class__.__name__, str(value))