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fix #1067 #2507

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Merged
merged 2 commits into from
Feb 22, 2018
Merged

fix #1067 #2507

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0c9598b
fix #1067
antgonza Feb 20, 2018
58858ae
addressing @ElDeveloper comments
antgonza Feb 21, 2018
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60 changes: 39 additions & 21 deletions qiita_db/environment_manager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,8 +53,8 @@ def _check_db_exists(db, conn_handler):
return (db,) in dbs


def create_layout_and_patch(test=False, verbose=False):
r"""Builds the SQL layout and applies all the patches
def create_layout(test=False, verbose=False):
r"""Builds the SQL layout

Parameters
----------
Expand All @@ -69,10 +69,6 @@ def create_layout_and_patch(test=False, verbose=False):
qdb.sql_connection.TRN.add(f.read())
qdb.sql_connection.TRN.execute()

if verbose:
print('Patching Database...')
patch(verbose=verbose, test=test)


def _populate_test_db():
with qdb.sql_connection.TRN:
Expand Down Expand Up @@ -191,30 +187,51 @@ def make_environment(load_ontologies, download_reference, add_demo_user):

# Create the database
print('Creating database')
create_settings_table = True
admin_conn.autocommit = True
admin_conn.execute('CREATE DATABASE %s' % qiita_config.database)
try:
admin_conn.execute('CREATE DATABASE %s' % qiita_config.database)
except ValueError as error:
# if database exists ignore
msg = 'database "%s" already exists' % qiita_config.database
if msg in error.message:
print("Database exits, let's make sure it's test")
with qdb.sql_connection.TRN:
# Insert the settings values to the database
sql = """SELECT test FROM settings"""
qdb.sql_connection.TRN.add(sql)
is_test = qdb.sql_connection.TRN.execute_fetchlast()
if not is_test:
print('Not a test database')
raise
create_settings_table = False
else:
raise
admin_conn.autocommit = False

del admin_conn
qdb.sql_connection.SQLConnectionHandler.close()

with qdb.sql_connection.TRN:
print('Inserting database metadata')
# Build the SQL layout into the database
with open(SETTINGS_FP, 'U') as f:
qdb.sql_connection.TRN.add(f.read())
qdb.sql_connection.TRN.execute()
test = qiita_config.test_environment
verbose = True
if create_settings_table:
# Build the SQL layout into the database
with open(SETTINGS_FP, 'U') as f:
qdb.sql_connection.TRN.add(f.read())
qdb.sql_connection.TRN.execute()

# Insert the settings values to the database
sql = """INSERT INTO settings (test, base_data_dir, base_work_dir)
VALUES (%s, %s, %s)"""
qdb.sql_connection.TRN.add(
sql, [qiita_config.test_environment, qiita_config.base_data_dir,
qiita_config.working_dir])
qdb.sql_connection.TRN.execute()
# Insert the settings values to the database
sql = """INSERT INTO settings (test, base_data_dir, base_work_dir)
VALUES (%s, %s, %s)"""
qdb.sql_connection.TRN.add(
sql, [test, qiita_config.base_data_dir,
qiita_config.working_dir])
qdb.sql_connection.TRN.execute()
create_layout(test=test, verbose=verbose)

create_layout_and_patch(test=qiita_config.test_environment,
verbose=True)
patch(verbose=verbose, test=test)

if load_ontologies:
_add_ontology_data()
Expand Down Expand Up @@ -315,7 +332,8 @@ def drop_and_rebuild_tst_database():
qdb.sql_connection.TRN.add(
"UPDATE settings SET current_patch = 'unpatched'")
# Create the database and apply patches
create_layout_and_patch(test=True)
create_layout(test=True)
patch(test=True)

qdb.sql_connection.TRN.execute()

Expand Down