def test_delete_job(self, mock_print, mock_bespin_api, mock_config_file):
commands = Commands(self.version_str, self.user_agent_str)
commands.delete_job(job_id=3)
self.assertFalse(mock_bespin_api.return_value.authorize_job.called)
mock_bespin_api.return_value.delete_job.assert_called_with(3)
mock_print.assert_has_calls([call("Deleted job 3")])
def test_workflow_create(self, mock_print, mock_bespin_api,
mock_config_file):
mock_bespin_api.return_value.workflow_post.return_value = {'id': 4}
commands = Commands(self.version_str, self.user_agent_str)
commands.workflow_create(name='myname', tag='mytag')
mock_bespin_api.return_value.workflow_post.assert_called_with(
'myname', 'mytag')
mock_print.assert_has_calls([call("Created workflow 4.")])
def test_start_job_no_token(self, mock_print, mock_bespin_api,
mock_config_file):
commands = Commands(self.version_str, self.user_agent_str)
commands.start_job(job_id=1)
self.assertFalse(mock_bespin_api.return_value.authorize_job.called)
mock_bespin_api.return_value.start_job.assert_called_with(1)
mock_print.assert_has_calls([call("Started job 1")])
def test_workflow_version_validate_raises_without_path(self):
commands = Commands(self.version_str, self.user_agent_str)
with self.assertRaises(UserInputException) as context:
commands.workflow_version_validate(url='someurl',
workflow_type='not-direct',
workflow_path=None,
expected_tag='workflow-tag',
expected_version='v1.2.3')
self.assertIn('path is required', str(context.exception))
def test_jobs_list(self, mock_print, mock_table, mock_jobs_list,
mock_bespin_api, mock_config_file):
commands = Commands(self.version_str, self.user_agent_str)
commands.jobs_list()
mock_jobs_list.assert_called_with(mock_bespin_api.return_value)
mock_table.assert_called_with(
mock_jobs_list.return_value.column_names,
mock_jobs_list.return_value.get_column_data.return_value)
mock_print.assert_called_with(mock_table.return_value)
def test_workflow_version_validate_direct_raises_if_path(self):
commands = Commands(self.version_str, self.user_agent_str)
with self.assertRaises(UserInputException) as context:
commands.workflow_version_validate(
url='someurl',
workflow_type='direct',
workflow_path='extracted/workflow.cwl',
expected_tag='workflow-tag',
expected_version='v1.2.3')
self.assertIn('Do not provide path', str(context.exception))
def test_start_job_with_token(self, mock_print, mock_bespin_api,
mock_config_file):
commands = Commands(self.version_str, self.user_agent_str)
commands.start_job(job_id=1, token='secret')
mock_bespin_api.return_value.authorize_job.assert_called_with(
1, 'secret')
mock_bespin_api.return_value.start_job.assert_called_with(1)
mock_print.assert_has_calls(
[call('Set run token for job 1'),
call('Started job 1')])
def test_job_validate_exception(self, mock_print, mock_job_template_loader,
mock_bespin_api, mock_config_file):
mock_infile = Mock()
mock_job_template = mock_job_template_loader.return_value.create_job_template.return_value
mock_job_template.validate.side_effect = UserInputException("Bad data")
commands = Commands(self.version_str, self.user_agent_str)
with self.assertRaises(UserInputException):
commands.job_validate(job_template_infile=mock_infile)
mock_print.assert_called_with('ERROR: Job template is invalid.')
def main():
version_str = pkg_resources.get_distribution(APP_NAME).version
user_agent_str = '{}_{}'.format(APP_NAME, version_str)
arg_parser = ArgParser(version_str, Commands(version_str, user_agent_str))
try:
arg_parser.parse_and_run_commands()
except ConfigSetupAbandoned:
pass
except UserInputException as e:
print(str(e))
sys.exit(1)
def test_job_template_create(self, mock_print, mock_bespin_api,
mock_config_file):
mock_outfile = Mock()
mock_bespin_api.return_value.job_templates_init.return_value = {}
commands = Commands(self.version_str, self.user_agent_str)
commands.job_template_create(tag='rnaseq/v1/human',
outfile=mock_outfile)
mock_bespin_api.return_value.job_templates_init.assert_called_with(
'rnaseq/v1/human')
mock_outfile.write.assert_called_with('{}\n')
def test_workflow_versions_list(self, mock_print, mock_table,
mock_workflow_versions_list,
mock_bespin_api, mock_config_file):
commands = Commands(self.version_str, self.user_agent_str)
commands.workflow_versions_list(workflow_tag='sometag')
mock_workflow_versions_list.assert_called_with(
mock_bespin_api.return_value, 'sometag')
mock_table.assert_called_with(
mock_workflow_versions_list.return_value.column_names,
mock_workflow_versions_list.return_value.get_column_data.
return_value)
mock_print.assert_called_with(mock_table.return_value)
def test_job_validate(self, mock_print, mock_job_template_loader,
mock_bespin_api, mock_config_file):
mock_infile = Mock()
commands = Commands(self.version_str, self.user_agent_str)
commands.job_validate(job_template_infile=mock_infile)
mock_job_template_loader.assert_called_with(mock_infile)
mock_job_template = mock_job_template_loader.return_value.create_job_template.return_value
mock_job_template.validate.assert_called_with(
mock_bespin_api.return_value)
mock_print.assert_called_with('Job file is valid.')
def test_workflows_list_all_versions(self, mock_print, mock_table,
mock_workflow_details,
mock_bespin_api, mock_config_file):
commands = Commands(self.version_str, self.user_agent_str)
commands.workflows_list(all_versions=True,
short_format=False,
tag=None)
workflow_details = mock_workflow_details.return_value
mock_table.assert_called_with(
workflow_details.column_names,
workflow_details.get_column_data.return_value)
mock_print.assert_called_with(mock_table.return_value)
mock_workflow_details.assert_called_with(mock_bespin_api.return_value,
True, None)
def test_workflow_config_show_job_order(self, mock_print, mock_bespin_api,
mock_config_file):
mock_outfile = Mock()
mock_bespin_api.return_value.workflow_configurations_list.return_value = [
{
"system_job_order": {
"threads": 2
}
}
]
commands = Commands(self.version_str, self.user_agent_str)
commands.workflow_config_show_job_order(tag="human",
workflow_tag="exomeseq",
outfile=mock_outfile)
mock_outfile.write.assert_called_with('threads: 2\n')
def test_workflow_version_validate(self, mock_cwl_workflow_version,
mock_print):
commands = Commands(self.version_str, self.user_agent_str)
mock_cwl_workflow_version.return_value.validate_workflow.return_value = Mock(
tag='workflow-tag', version='v1.2.3')
commands.workflow_version_validate(
url='someurl',
workflow_type='zipped',
workflow_path='extracted/workflow.cwl',
expected_tag='workflow-tag',
expected_version='v1.2.3')
mock_cwl_workflow_version.assert_called_with('someurl',
'zipped',
'extracted/workflow.cwl',
validate=True)
mock_print.assert_has_calls(
[call("Validated someurl as 'workflow-tag/v1.2.3'")])
def test_job_create(self, mock_print, mock_job_template_loader,
mock_bespin_api, mock_config_file):
mock_infile = Mock()
mock_job_template_loader.return_value.create_job_template.return_value.create_job.return_value = {
'job': 1
}
commands = Commands(self.version_str, self.user_agent_str)
commands.job_create(job_template_infile=mock_infile)
mock_job_template_loader.assert_called_with(mock_infile)
mock_print.assert_has_calls([
call("Created job 1"),
call("To start this job run `bespin job start 1` .")
])
mock_job_template = mock_job_template_loader.return_value.create_job_template.return_value
mock_job_template.create_job.assert_called_with(
mock_bespin_api.return_value)
def test_job_run(self, mock_print, mock_job_template_loader,
mock_bespin_api, mock_config_file):
mock_infile = Mock()
mock_job_template_loader.return_value.create_job_template.return_value.create_job.return_value = {
'job': 1
}
commands = Commands(self.version_str, self.user_agent_str)
commands.job_run(job_template_infile=mock_infile, token='mytoken')
mock_job_template_loader.assert_called_with(mock_infile)
mock_print.assert_has_calls([
call("Created job 1"),
call("Set run token for job 1"),
call("Started job 1")
])
mock_job_template = mock_job_template_loader.return_value.create_job_template.return_value
mock_job_template.create_job.assert_called_with(
mock_bespin_api.return_value)
def test_workflow_version_create(self, mock_cwl_workflow_version,
mock_print, mock_bespin_api,
mock_config_file):
mock_cwl_workflow_version.return_value.create.return_value = {'id': 7}
commands = Commands(self.version_str, self.user_agent_str)
commands.workflow_version_create(url='someurl',
workflow_type='packed',
workflow_path='#main',
version_info_url='infourl',
override_version='v3.2',
override_tag='tag',
validate=True)
mock_cwl_workflow_version.assert_called_with('someurl',
'packed',
'#main',
'infourl',
override_tag='tag',
override_version='v3.2',
validate=True)
mock_print.assert_has_calls([call("Created workflow version 7.")])
def test_workflow_version_tool_details_preview(self, mock_tool_details,
mock_cwl_workflow_version,
mock_json, mock_print):
commands = Commands(self.version_str, self.user_agent_str)
mock_cwl_workflow_version.return_value.validate_workflow.return_value = Mock(
tag='workflow-tag', version='v1.2.3')
commands.workflow_version_tool_details_preview(
url='someurl',
workflow_type='zipped',
workflow_path='extracted/workflow.cwl')
mock_cwl_workflow_version.assert_called_with('someurl',
'zipped',
'extracted/workflow.cwl',
override_tag=None,
override_version=None,
validate=False)
mock_tool_details.assert_called_with(
mock_cwl_workflow_version.return_value)
mock_json.dumps.assert_called_with(
mock_tool_details.return_value.contents, indent=2)
mock_print.assert_called_with(mock_json.dumps.return_value)
def test_workflow_version_tool_details_create(self, mock_tool_details,
mock_cwl_workflow_version,
mock_print, mock_bespin_api,
mock_config_file):
commands = Commands(self.version_str, self.user_agent_str)
mock_create = mock_tool_details.return_value.create
mock_create.return_value = {'id': '5'}
commands.workflow_version_tool_details_create(
url='someurl',
workflow_type='zipped',
workflow_path='extracted/workflow.cwl',
override_tag='tagg',
override_version='v1')
mock_cwl_workflow_version.assert_called_with('someurl',
'zipped',
'extracted/workflow.cwl',
override_tag='tagg',
override_version='v1',
validate=False)
mock_create.assert_called_with(mock_bespin_api.return_value)
mock_print.assert_called_with(
"Created workflow version tool details 5.")
def test_workflow_config_create(self, mock_yaml, mock_print,
mock_bespin_api, mock_config_file):
mock_yaml.load.return_value = {'a': 1}
mock_bespin_api.return_value.workflow_get_for_tag.return_value = {
'id': 2
}
mock_bespin_api.return_value.job_strategy_get_for_name.return_value = {
'id': 3
}
mock_bespin_api.return_value.share_group_get_for_name.return_value = {
'id': 4
}
mock_bespin_api.return_value.workflow_configurations_post.return_value = {
'id': 5
}
commands = Commands(self.version_str, self.user_agent_str)
commands.workflow_config_create(workflow_tag='exome',
default_job_strategy_name='default',
share_group_name='myname',
tag='human',
joborder_infile=Mock())
mock_bespin_api.return_value.workflow_configurations_post.assert_called_with(
'human', 2, 3, 4, {'a': 1})
mock_print.assert_called_with("Created workflow config 5.")