def testCreateTable(self):
connection,cursor = self.connection_tuple
tablename='test'
tablestring = ('CREATE TABLE {name} '
'(id text PRIMARY KEY, '
'year integer, '
'data jsonb);'
.format(name=tablename)
)
setup_db.create_table(connection,cursor,tablename,tablestring)
assert setup_db.table_exists(cursor, tablename) == True
def testDeleteTable(self):
connection,cursor = self.connection_tuple
tablename='test'
assert setup_db.table_exists(cursor, tablename) == True
setup_db.delete_table(connection,cursor,tablename)
assert setup_db.table_exists(cursor, tablename) == False
args = parser.parse_args()
# read config variables
config_obj = setup_db.read_config(args.configfile)
connection, cursor = setup_db.connect(config_obj)
# test that tables exist
# and clear data, except taxonomy table
try:
tabledict = dict(config_obj.items('database_tables'))
for table in tabledict:
# skip the taxonomy table, which does note get loaded here
if table == "otttable":
continue
name = tabledict[table]
if setup_db.table_exists(cursor,name):
setup_db.clear_single_table(connection,cursor,name)
else:
raise psy.ProgrammingError("Table {t} does not exist".format(t=name))
setup_db.clear_gin_index(connection,cursor)
print "done clearing tables and index"
except psy.Error as e:
print e.pgerror
# data import
starttime = dt.datetime.now()
try:
# TODO: catch peyotl-specific exceptions
phy = create_phylesystem_obj()
print "loading nexsons"
if (args.nstudies):