def workflow_create(ctx, file, name, skip_validation,
access_token): # noqa: D301
"""Create a new workflow.
The `create` command allows to create a new workflow from reana.yaml
specifications file. The file is expected to be located in the current
working directory, or supplied via command-line -f option, see examples
below.
Examples: \n
\t $ reana-client create\n
\t $ reana-client create -w myanalysis\n
\t $ reana-client create -w myanalysis -f myreana.yaml\n
"""
logging.debug('command: {}'.format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug('{param}: {value}'.format(param=p, value=ctx.params[p]))
# Check that name is not an UUIDv4.
# Otherwise it would mess up `--workflow` flag usage because no distinction
# could be made between the name and actual UUID of workflow.
if is_uuid_v4(name):
click.echo(click.style('Workflow name cannot be a valid UUIDv4',
fg='red'),
err=True)
if not access_token:
click.echo(click.style(ERROR_MESSAGES['missing_access_token'],
fg='red'),
err=True)
sys.exit(1)
try:
reana_specification = load_reana_spec(click.format_filename(file),
skip_validation)
logging.info('Connecting to {0}'.format(
current_rs_api_client.swagger_spec.api_url))
response = create_workflow(reana_specification, name, access_token)
click.echo(click.style(response['workflow_name'], fg='green'))
# check if command is called from wrapper command
if 'invoked_by_subcommand' in ctx.parent.__dict__:
ctx.parent.workflow_name = response['workflow_name']
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(click.style('Workflow could not be created: \n{}'.format(
str(e)),
fg='red'),
err=True)
if 'invoked_by_subcommand' in ctx.parent.__dict__:
sys.exit(1)
def workflow_create(ctx, file, name, skip_validation,
access_token): # noqa: D301
"""Create a new workflow.
The `create` command allows to create a new workflow from reana.yaml
specifications file. The file is expected to be located in the current
working directory, or supplied via command-line -f option, see examples
below.
Examples: \n
\t $ reana-client create\n
\t $ reana-client create -w myanalysis\n
\t $ reana-client create -w myanalysis -f myreana.yaml\n
"""
from reana_client.api.client import create_workflow
from reana_client.utils import get_api_url
logging.debug("command: {}".format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug("{param}: {value}".format(param=p, value=ctx.params[p]))
# Check that name is not an UUIDv4.
# Otherwise it would mess up `--workflow` flag usage because no distinction
# could be made between the name and actual UUID of workflow.
if is_uuid_v4(name):
click.echo(click.style("Workflow name cannot be a valid UUIDv4",
fg="red"),
err=True)
try:
reana_specification = load_reana_spec(click.format_filename(file),
skip_validation)
logging.info("Connecting to {0}".format(get_api_url()))
response = create_workflow(reana_specification, name, access_token)
click.echo(click.style(response["workflow_name"], fg="green"))
# check if command is called from wrapper command
if "invoked_by_subcommand" in ctx.parent.__dict__:
ctx.parent.workflow_name = response["workflow_name"]
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(
click.style("Cannot create workflow {}: \n{}".format(name, str(e)),
fg="red"),
err=True,
)
if "invoked_by_subcommand" in ctx.parent.__dict__:
sys.exit(1)
def workflow_create(ctx, file, name, skip_validation, access_token):
"""Create a REANA compatible workflow from REANA spec file."""
logging.debug('command: {}'.format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug('{param}: {value}'.format(param=p, value=ctx.params[p]))
# Check that name is not an UUIDv4.
# Otherwise it would mess up `--workflow` flag usage because no distinction
# could be made between the name and actual UUID of workflow.
if is_uuid_v4(name):
click.echo(
click.style('Workflow name cannot be a valid UUIDv4', fg='red'),
err=True)
if not access_token:
click.echo(
click.style(ERROR_MESSAGES['missing_access_token'],
fg='red'), err=True)
sys.exit(1)
try:
reana_specification = load_reana_spec(click.format_filename(file),
skip_validation)
logging.info('Connecting to {0}'.format(
current_rs_api_client.swagger_spec.api_url))
response = create_workflow(reana_specification,
name,
access_token)
click.echo(click.style(response['workflow_name'], fg='green'))
# check if command is called from wrapper command
if 'invoked_by_subcommand' in ctx.parent.__dict__:
ctx.parent.workflow_name = response['workflow_name']
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(
click.style('Workflow could not be created: \n{}'
.format(str(e)), fg='red'),
err=True)
if 'invoked_by_subcommand' in ctx.parent.__dict__:
sys.exit(1)
def create_workflow_from_json(
name,
access_token,
workflow_json=None,
workflow_file=None,
parameters=None,
workflow_engine="yadage",
outputs=None,
):
"""Create a workflow from json specification.
:param name: name or UUID of the workflow to be started.
:param access_token: access token of the current user.
:param workflow_json: workflow specification in json format.
:param workflow_file: workflow specification file path.
Ignores ``workflow_json`` if provided.
:param parameters: workflow input parameters dictionary.
:param workflow_engine: one of the workflow engines (yadage, serial, cwl)
:param outputs: dictionary with expected workflow outputs.
:Example:
.. code:: python
create_workflow_from_json(
workflow_json=workflow_json,
name='workflow_name.1',
access_token='access_token',
parameters={'files': ['file.txt'], 'parameters': {'key': 'value'}},
workflow_engine='serial')
"""
validate_workflow_name(name)
if is_uuid_v4(name):
raise ValueError("Workflow name cannot be a valid UUIDv4")
if not access_token:
raise Exception(ERROR_MESSAGES["missing_access_token"])
if os.environ.get("REANA_SERVER_URL") is None:
raise Exception("Environment variable REANA_SERVER_URL is not set")
workflow_engine = workflow_engine.lower()
if workflow_engine not in REANA_WORKFLOW_ENGINES:
raise Exception("Workflow engine - {} not found. You must use one of "
"these engines - {}".format(workflow_engine,
REANA_WORKFLOW_ENGINES))
try:
reana_yaml = dict(workflow={})
if workflow_file:
reana_yaml["workflow"]["file"] = workflow_file
else:
reana_yaml["workflow"]["specification"] = workflow_json
reana_yaml["workflow"]["type"] = workflow_engine
if parameters:
reana_yaml["inputs"] = parameters
if outputs:
reana_yaml["outputs"] = outputs
_validate_reana_yaml(reana_yaml)
reana_specification = reana_yaml
(response, http_response) = current_rs_api_client.api.create_workflow(
reana_specification=json.loads(
json.dumps(reana_specification, sort_keys=True)),
workflow_name=name,
access_token=access_token,
).result()
if http_response.status_code == 201:
return response
else:
raise Exception(
"Expected status code 201 but replied with "
"{status_code}".format(status_code=http_response.status_code))
except HTTPError as e:
logging.debug("Workflow creation failed: "
"\nStatus: {}\nReason: {}\n"
"Message: {}".format(e.response.status_code,
e.response.reason,
e.response.json()["message"]))
raise Exception(e.response.json()["message"])
except Exception as e:
raise e
def create_workflow_from_json(workflow_json, name, access_token,
parameters=None, workflow_engine='yadage',
outputs=None):
"""Create a workflow from json specification.
:param workflow_json: workflow specification in json format.
:param name: name or UUID of the workflow to be started.
:param access_token: Access token of the current user.
:param parameters: workflow input parameters dictionary.
:param workflow_engine: one of the workflow engines (yadage, serial, cwl)
:param outputs: dictionary with expected workflow outputs.
:Example:
.. code:: python
create_workflow_from_json(
workflow_json=workflow_json,
name='workflow_name.1',
access_token='access_token',
parameters={'files': ['file.txt'], 'parameters': {'key': 'value'}},
workflow_engine='serial')
"""
if is_uuid_v4(name):
raise ValueError('Workflow name cannot be a valid UUIDv4')
if not access_token:
raise Exception(ERROR_MESSAGES['missing_access_token'])
if os.environ.get('REANA_SERVER_URL') is None:
raise Exception('Environment variable REANA_SERVER_URL is not set')
workflow_engine = workflow_engine.lower()
if workflow_engine not in WORKFLOW_ENGINES:
raise Exception('Workflow engine - {} not found. You must use one of '
'these engines - {}'.format(workflow_engine,
WORKFLOW_ENGINES))
try:
reana_yaml = {}
reana_yaml['workflow'] = {'specification': workflow_json}
reana_yaml['workflow']['type'] = workflow_engine
if parameters:
reana_yaml['inputs'] = parameters
if outputs:
reana_yaml['outputs'] = outputs
_validate_reana_yaml(reana_yaml)
reana_specification = reana_yaml
(response,
http_response) = current_rs_api_client.api.create_workflow(
reana_specification=json.loads(json.dumps(
reana_specification, sort_keys=True)),
workflow_name=name,
access_token=access_token).result()
if http_response.status_code == 201:
return response
else:
raise Exception(
"Expected status code 201 but replied with "
"{status_code}".format(
status_code=http_response.status_code))
except HTTPError as e:
logging.debug(
'Workflow creation failed: '
'\nStatus: {}\nReason: {}\n'
'Message: {}'.format(e.response.status_code,
e.response.reason,
e.response.json()['message']))
raise Exception(e.response.json()['message'])
except Exception as e:
raise e