def _prepare_kwargs(reana_yaml):
kwargs = {}
workflow_type = reana_yaml["workflow"]["type"]
if workflow_type == "serial":
kwargs["specification"] = reana_yaml["workflow"].get(
"specification")
kwargs["parameters"] = reana_yaml.get("inputs",
{}).get("parameters", {})
kwargs["original"] = True
if "options" in reana_yaml.get("inputs", {}):
try:
reana_yaml["inputs"]["options"] = validate_operational_options(
workflow_type, reana_yaml["inputs"]["options"])
except REANAValidationError as e:
click.secho(e.message, err=True, fg="red")
sys.exit(1)
kwargs.update(reana_yaml["inputs"]["options"])
return kwargs
def _prepare_kwargs(reana_yaml):
kwargs = {}
workflow_type = reana_yaml["workflow"]["type"]
if workflow_type == "serial":
kwargs["specification"] = reana_yaml["workflow"].get(
"specification")
kwargs["parameters"] = reana_yaml.get("inputs",
{}).get("parameters", {})
kwargs["original"] = True
if "options" in reana_yaml.get("inputs", {}):
try:
reana_yaml["inputs"]["options"] = validate_operational_options(
workflow_type, reana_yaml["inputs"]["options"])
except REANAValidationError as e:
display_message(e.message, msg_type="error")
sys.exit(1)
kwargs.update(reana_yaml["inputs"]["options"])
if workflow_type == "snakemake":
kwargs["input"] = (reana_yaml.get("inputs",
{}).get("parameters",
{}).get("input"))
return kwargs
def workflow_restart(
ctx, workflow, access_token, parameters, options, file
): # noqa: D301
"""Restart previously run workflow.
The ``restart`` command allows to restart a previous workflow on the same
workspace.
Note that workflow restarting can be used in a combination with operational
options ``FROM`` and ``TARGET``. You can also pass a modified workflow
specification with ``-f`` or ``--file`` flag.
You can furthermore use modified input prameters using ``-p`` or
``--parameters`` flag and by setting additional operational options using
``-o`` or ``--options``. The input parameters and operational options can be
repetitive.
Examples: \n
\t $ reana-client restart -w myanalysis.42 -p sleeptime=10 -p myparam=4 \n
\t $ reana-client restart -w myanalysis.42 -p myparam=myvalue\n
\t $ reana-client restart -w myanalysis.42 -o TARGET=gendata\n
\t $ reana-client restart -w myanalysis.42 -o FROM=fitdata
"""
from reana_client.utils import get_api_url
from reana_client.api.client import (
get_workflow_parameters,
get_workflow_status,
start_workflow,
)
logging.debug("command: {}".format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug("{param}: {value}".format(param=p, value=ctx.params[p]))
parsed_parameters = {
"input_parameters": parameters,
"operational_options": options,
"restart": True,
}
if file:
parsed_parameters["reana_specification"] = load_reana_spec(
click.format_filename(file)
)
if workflow:
if parameters or options:
try:
if "reana_specification" in parsed_parameters:
workflow_type = parsed_parameters["reana_specification"][
"workflow"
]["type"]
original_parameters = (
parsed_parameters["reana_specification"]
.get("inputs", {})
.get("parameters", {})
)
else:
response = get_workflow_parameters(workflow, access_token)
workflow_type = response["type"]
original_parameters = response["parameters"]
parsed_parameters["operational_options"] = validate_operational_options(
workflow_type, parsed_parameters["operational_options"]
)
parsed_parameters["input_parameters"] = validate_input_parameters(
parsed_parameters["input_parameters"], original_parameters
)
except REANAValidationError as e:
display_message(e.message, msg_type="error")
sys.exit(1)
except Exception as e:
display_message(
"Could not apply given input parameters: "
"{0} \n{1}".format(parameters, str(e)),
msg_type="error",
)
try:
logging.info("Connecting to {0}".format(get_api_url()))
response = start_workflow(workflow, access_token, parsed_parameters)
workflow = response["workflow_name"] + "." + str(response["run_number"])
current_status = get_workflow_status(workflow, access_token).get("status")
display_message(
get_workflow_status_change_msg(workflow, current_status),
msg_type="success",
)
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
display_message(
"Cannot start workflow {}: \n{}".format(workflow, str(e)),
msg_type="error",
)
if "invoked_by_subcommand" in ctx.parent.__dict__:
sys.exit(1)
def workflow_start(
ctx, workflow, access_token, parameters, options, follow
): # noqa: D301
"""Start previously created workflow.
The ``start`` command allows to start previously created workflow. The
workflow execution can be further influenced by passing input prameters
using ``-p`` or ``--parameters`` flag and by setting additional operational
options using ``-o`` or ``--options``. The input parameters and operational
options can be repetitive. For example, to disable caching for the Serial
workflow engine, you can set ``-o CACHE=off``.
Examples: \n
\t $ reana-client start -w myanalysis.42 -p sleeptime=10 -p myparam=4 \n
\t $ reana-client start -w myanalysis.42 -p myparam1=myvalue1 -o CACHE=off
"""
from reana_client.utils import get_api_url
from reana_client.api.client import (
get_workflow_parameters,
get_workflow_status,
start_workflow,
)
logging.debug("command: {}".format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug("{param}: {value}".format(param=p, value=ctx.params[p]))
parsed_parameters = {"input_parameters": parameters, "operational_options": options}
if workflow:
if parameters or options:
try:
response = get_workflow_parameters(workflow, access_token)
workflow_type = response["type"]
original_parameters = response["parameters"]
validate_operational_options(
workflow_type, parsed_parameters["operational_options"]
)
parsed_parameters["input_parameters"] = validate_input_parameters(
parsed_parameters["input_parameters"], original_parameters
)
except REANAValidationError as e:
display_message(e.message, msg_type="error")
sys.exit(1)
except Exception as e:
display_message(
"Could not apply given input parameters: "
"{0} \n{1}".format(parameters, str(e)),
msg_type="error",
)
try:
logging.info("Connecting to {0}".format(get_api_url()))
response = start_workflow(workflow, access_token, parsed_parameters)
current_status = get_workflow_status(workflow, access_token).get("status")
display_message(
get_workflow_status_change_msg(workflow, current_status),
msg_type="success",
)
if follow:
while "running" in current_status:
time.sleep(TIMECHECK)
current_status = get_workflow_status(workflow, access_token).get(
"status"
)
display_message(
get_workflow_status_change_msg(workflow, current_status),
msg_type="success",
)
if "finished" in current_status:
if follow:
display_message(
"Listing workflow output files...", msg_type="info",
)
ctx.invoke(
get_files,
workflow=workflow,
access_token=access_token,
output_format="url",
)
sys.exit(0)
elif "failed" in current_status or "stopped" in current_status:
sys.exit(1)
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
display_message(
"Cannot start workflow {}: \n{}".format(workflow, str(e)),
msg_type="error",
)
if "invoked_by_subcommand" in ctx.parent.__dict__:
sys.exit(1)
def test_successful(workflow_type, options, option):
"""Test successful operational options cases."""
validated_options = validate_operational_options(workflow_type, options)
assert validated_options[option]
def test_unsupported(workflow_type, options, except_msg):
"""Test unsupported operational options cases."""
with pytest.raises(REANAValidationError) as e:
validate_operational_options(workflow_type, options)
assert except_msg.format(workflow_type=workflow_type) in e.value.message
def workflow_restart(ctx, workflow, access_token, parameters, options,
file): # noqa: D301
"""Restart previously run workflow.
The `restart` command allows to restart a previous workflow on the same
workspace.
Note that workflow restarting can be used in a combination with operational
options ``FROM`` and ``TARGET``. You can also pass a modified workflow
specification with ``-f`` or `--file`` flag.
You can furthermore use modified input prameters using `-p` or
`--parameters` flag and by setting additional operational options using
`-o` or `--options`. The input parameters and operational options can be
repetitive.
Examples: \n
\t $ reana-client restart -w myanalysis.42 -p sleeptime=10 -p myparam=4 \n
\t $ reana-client restart -w myanalysis.42 -p myparam=myvalue\n
\t $ reana-client restart -w myanalysis.42 -o TARGET=gendata\n
\t $ reana-client restart -w myanalysis.42 -o FROM=fitdata
"""
from reana_client.utils import get_api_url
from reana_client.api.client import (get_workflow_parameters,
get_workflow_status, start_workflow)
logging.debug('command: {}'.format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug('{param}: {value}'.format(param=p, value=ctx.params[p]))
parsed_parameters = {
'input_parameters': parameters,
'operational_options': options,
'restart': True
}
if file:
parsed_parameters['reana_specification'] = \
load_reana_spec(click.format_filename(file))
if workflow:
if parameters or options:
try:
if 'reana_specification' in parsed_parameters:
workflow_type = \
parsed_parameters['reana_specification']['workflow'][
'type']
original_parameters = \
parsed_parameters['reana_specification'].get(
'inputs', {}).get('parameters', {})
else:
response = get_workflow_parameters(workflow, access_token)
workflow_type = response['type']
original_parameters = response['parameters']
parsed_parameters['operational_options'] = \
validate_operational_options(
workflow_type,
parsed_parameters['operational_options'])
parsed_parameters['input_parameters'] = \
validate_input_parameters(
parsed_parameters['input_parameters'],
original_parameters)
except REANAValidationError as e:
click.secho(e.message, err=True, fg='red')
sys.exit(1)
except Exception as e:
click.secho('Could not apply given input parameters: '
'{0} \n{1}'.format(parameters, str(e)),
err=True)
try:
logging.info('Connecting to {0}'.format(get_api_url()))
response = start_workflow(workflow, access_token,
parsed_parameters)
workflow = response['workflow_name'] + '.' + \
str(response['run_number'])
current_status = get_workflow_status(workflow,
access_token).get('status')
click.secho(get_workflow_status_change_msg(workflow,
current_status),
fg='green')
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(click.style('Cannot start workflow {}: \n{}'.format(
workflow, str(e)),
fg='red'),
err=True)
if 'invoked_by_subcommand' in ctx.parent.__dict__:
sys.exit(1)
def workflow_start(ctx, workflow, access_token, parameters, options,
follow): # noqa: D301
"""Start previously created workflow.
The `start` command allows to start previously created workflow. The
workflow execution can be further influenced by passing input prameters
using `-p` or `--parameters` flag and by setting additional operational
options using `-o` or `--options`. The input parameters and operational
options can be repetitive. For example, to disable caching for the Serial
workflow engine, you can set `-o CACHE=off`.
Examples: \n
\t $ reana-client start -w myanalysis.42 -p sleeptime=10 -p myparam=4 \n
\t $ reana-client start -w myanalysis.42 -p myparam1=myvalue1 -o CACHE=off
"""
from reana_client.utils import get_api_url
from reana_client.api.client import (get_workflow_parameters,
get_workflow_status, start_workflow)
logging.debug('command: {}'.format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug('{param}: {value}'.format(param=p, value=ctx.params[p]))
parsed_parameters = {
'input_parameters': parameters,
'operational_options': options
}
if workflow:
if parameters or options:
try:
response = get_workflow_parameters(workflow, access_token)
workflow_type = response['type']
original_parameters = response['parameters']
validate_operational_options(
workflow_type, parsed_parameters['operational_options'])
parsed_parameters['input_parameters'] = \
validate_input_parameters(
parsed_parameters['input_parameters'],
original_parameters)
except REANAValidationError as e:
click.secho(e.message, err=True, fg='red')
sys.exit(1)
except Exception as e:
click.secho('Could not apply given input parameters: '
'{0} \n{1}'.format(parameters, str(e)),
err=True)
try:
logging.info('Connecting to {0}'.format(get_api_url()))
response = start_workflow(workflow, access_token,
parsed_parameters)
current_status = get_workflow_status(workflow,
access_token).get('status')
click.secho(get_workflow_status_change_msg(workflow,
current_status),
fg='green')
if follow:
while 'running' in current_status:
time.sleep(TIMECHECK)
current_status = get_workflow_status(
workflow, access_token).get('status')
click.secho(get_workflow_status_change_msg(
workflow, current_status),
fg='green')
if 'finished' in current_status:
if follow:
click.secho(
'[INFO] Listing workflow output '
'files...',
bold=True)
ctx.invoke(get_files,
workflow=workflow,
access_token=access_token,
output_format='url')
sys.exit(0)
elif 'failed' in current_status or \
'stopped' in current_status:
sys.exit(1)
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(click.style('Cannot start workflow {}: \n{}'.format(
workflow, str(e)),
fg='red'),
err=True)
if 'invoked_by_subcommand' in ctx.parent.__dict__:
sys.exit(1)