def remap(table, auto_confirmation=True, verify_definitions=False):
'''Applies change made in mapping protocols to database'''
table = gen_data_table(table, META)
table.gen_definitions()
table.map_from_database()
table.remap(auto_confirmation, verify_definitions)
def create(table, ignore_definitions=False):
'''Creates table from mapping_protocol metadata'''
table = gen_data_table(table, META)
table.gen_definitions()
with ENGINE.connect() as connection:
trans = connection.begin()
table.create(bind=connection, ignore_definitions=ignore_definitions)
table.set_source(bind=connection)
table.create_mapping_table(bind=connection)
trans.commit()
def csv_from_tabbed(table_name, input_file, output_file, year, sep=';'):
table = gen_data_table(table_name, META)
protocol = table.get_protocol()
column_names, column_mappings = protocol.get_tabbed_mapping(year)
copy_tabbed_to_csv(input_file,
column_mappings,
settings.CHUNK_SIZE,
output_file,
column_names=column_names,
sep=sep)
def run_aggregations(table, year):
'''
Runs aggregation queries from protocol
'''
table = gen_data_table(table, META)
table.map_from_database()
with ENGINE.connect() as connection:
trans = connection.begin()
table.run_aggregations(year, bind=connection)
trans.commit()
def insert(file_name,
table,
year,
offset=2,
delimiters=[';', '\\n', '"'],
null='',
notifybackup=None):
'''Inserts contents of csv in file_name in table using year as index for mapping'''
table = gen_data_table(table, META)
table.map_from_database()
if not table.exists():
raise MissingTableError(table.name)
with ENGINE.connect() as connection:
trans = connection.begin()
ttable = temporary_data(connection, file_name, table, year, offset,
delimiters, null)
table.insert_from_temporary(ttable, bind=connection)
trans.commit()
def update_from_file(file_name,
table,
year,
columns=None,
offset=2,
delimiters=[';', '\\n', '"'],
null=''):
'''Updates table columns from an input csv file'''
table = gen_data_table(table, META)
table.map_from_database()
if not table.exists():
raise MissingTableError(table.name)
if columns is None:
columns = [c.name for c in table.columns]
with ENGINE.connect() as connection:
trans = connection.begin()
ttable = temporary_data(connection, file_name, table, year, offset,
delimiters, null)
table.update_from_temporary(ttable, columns, bind=connection)
trans.commit()
def drop(table):
'''Drops table'''
table = gen_data_table(table, META)
table.drop()