def test_ErrorTableNotInDB(tmpdir):
'''Test the class ErrorTableNotInDB (error when a table doesn't exist in a database)'''
# This file is not created, just a tmp path
tmpfile = os.path.join(tmpdir.strpath, "tmpfile")
# Test instantiation
test_error = NCBImetaErrors.ErrorTableNotInDB(tmpfile)
# Test str representation (error message)
error_output = str(test_error)
error_expect = ("\n\nThe table does not exist in the database." + "\n" + "Unknown table found: " + tmpfile)
assert error_output == error_expect
raise NCBImetaErrors.ErrorAnnotFileNotExists(annot_file_name)
# no errors were raised, safe to connect to db
cur = conn.cursor()
#---------------------------Check Table---------------------------------#
# Check table name
table_name = db_table
table_name_sanitize = NCBImetaUtilities.sql_sanitize(table_name)
if table_name != table_name_sanitize:
raise NCBImetaErrors.ErrorSQLNameSanitize(table_name, table_name_sanitize)
# Check table exists
if not NCBImetaUtilities.table_exists(cur, db_table):
raise NCBImetaErrors.ErrorTableNotInDB(db_table)
#-----------------------------------------------------------------------#
# File Setup #
#-----------------------------------------------------------------------#
# get list of column names in Table
cur.execute('''SELECT * FROM {}'''.format(db_table))
db_col_names = [description[0] for description in cur.description]
#-----------------------------------------------------------------------#
# Annotation Setup #
#-----------------------------------------------------------------------#
annot_file = open(annot_file_name, "r")
annot_dict = {}
for table_name in table_name_list:
table_name_sanitize = NCBImetaUtilities.sql_sanitize(table_name)
if table_name != table_name_sanitize:
raise NCBImetaErrors.ErrorSQLNameSanitize(table_name,
table_name_sanitize)
# Check the column names
for col_name in unique_header_list:
col_name_sanitize = NCBImetaUtilities.sql_sanitize(col_name)
if col_name != col_name_sanitize:
raise NCBImetaErrors.ErrorSQLNameSanitize(col_name, col_name_sanitize)
#---------------------------Check Tables Existence----------------------#
if not NCBImetaUtilities.table_exists(cur, db_anchor):
raise NCBImetaErrors.ErrorTableNotInDB(db_anchor)
for table in db_accessory_list:
if not NCBImetaUtilities.table_exists(cur, table):
raise NCBImetaErrors.ErrorTableNotInDB(table)
#-----------------------------------------------------------------------#
# File Setup #
#-----------------------------------------------------------------------#
# get list of column names in anchor table
cur.execute('''SELECT * FROM {}'''.format(db_anchor))
db_col_names = [
description[0] for description in cur.description if description[0] != "id"
]
anchor_col_names = [description[0] for description in cur.description]
