def test_check_or_fail_succeed(self):
'''Check that check_or_fail succeeds properly.
'''
try:
databases.check_or_fail(self.handler)
except SystemExit:
assert False, 'Should not have exited'
def test_check_or_fail_fail(self, tmpdir):
config = self.config.copy()
config['database_dir'] = str(tmpdir)
handler = databases.get_handler(config)
databases.build_default_pipeline(handler,
config,
self.databases,
with_uniref=False)
with pytest.raises(SystemExit):
databases.check_or_fail(handler)
def handle_databases(self):
log.start_logging()
print(ui.header('submodule: databases', level=2))
handler = databases.get_handler(self.config_d)
if self.args.quick:
databases.build_quick_pipeline(handler, self.config_d,
self.databases_d)
else:
databases.build_default_pipeline(handler,
self.config_d,
self.databases_d,
with_uniref=self.args.full,
with_nr=self.args.nr)
if self.args.install:
return databases.install(handler)
else:
databases.check_or_fail(handler)
def handle_annotate(self):
log.start_logging()
print(ui.header('submodule: annotate', level=2))
db_handler = databases.get_handler(self.config_d)
if self.args.quick:
databases.build_quick_pipeline(db_handler, self.config_d,
self.databases_d)
else:
databases.build_default_pipeline(db_handler,
self.config_d,
self.databases_d,
with_uniref=self.args.full,
with_nr=self.args.nr)
if self.config_d['force'] is True:
utd_msg = '*All database tasks up-to-date.*'
ood_msg = '*Some database tasks out-of-date; '\
'FORCE is True, ignoring!'
uptodate, statuses = db_handler.print_statuses(
uptodate_msg=utd_msg, outofdate_msg=ood_msg)
else:
databases.check_or_fail(db_handler)
annotate_handler = annotate.get_handler(self.config_d,
db_handler.files)
if self.args.quick:
build_quick_pipeline(annotate_handler, self.config_d,
db_handler.files)
elif self.args.full:
build_full_pipeline(annotate_handler, self.config_d,
db_handler.files)
elif self.args.nr:
build_nr_pipeline(annotate_handler, self.config_d,
db_handler.files)
else:
build_default_pipeline(annotate_handler, self.config_d,
db_handler.files)
return annotate.run_annotation(annotate_handler)