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Made nf-core launch prompts beautiful #256

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Merged
sven1103 merged 1 commit into from
Jan 24, 2019
Merged

Made nf-core launch prompts beautiful #256

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129 changes: 92 additions & 37 deletions nf_core/launch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ def launch_pipeline(workflow, params_local_uri, direct):
params_list = []
try:
if params_local_uri:
with open(params_local_uri, 'r') as fp: params_json_str = fp.read()
with open(params_local_uri, 'r') as fp: params_json_str = fp.read()
else:
params_json_str = nf_core.utils.fetch_parameter_settings_from_github(workflow)
params_list = pms.Parameters.create_from_json(params_json_str)
Expand All @@ -43,10 +43,10 @@ def __init__(self, workflow):

self.workflow = workflow
self.nxf_flag_defaults = {
'-name': False,
'-r': False,
'-name': None,
'-r': None,
'-profile': 'standard',
'-w': os.getenv('NXF_WORK') if os.getenv('NXF_WORK') else 'work',
'-w': os.getenv('NXF_WORK') if os.getenv('NXF_WORK') else './work',
'-resume': False
}
self.nxf_flag_help = {
Expand All @@ -72,9 +72,29 @@ def collect_defaults(self):
def prompt_vars(self, params = None, direct = False):
""" Ask the user if they want to override any default values """
# Main nextflow flags
logging.info("Main nextflow options:\n")
click.secho("Main nextflow options", bold=True, underline=True)
for flag, f_default in self.nxf_flag_defaults.items():
f_user = click.prompt(self.nxf_flag_help[flag], default=f_default)

# Click prompts don't like None, so we have to use an empty string instead
f_default_print = f_default
if f_default is None:
f_default = ''
f_default_print = 'None'

# Overwrite the default prompt for boolean
if isinstance(f_default, bool):
f_default_print = 'Y/n' if f_default else 'y/N'

# Prompt for a response
f_user = click.prompt(
"\n{}\n {} {}".format(
self.nxf_flag_help[flag],
click.style(flag, fg='blue'),
click.style('[{}]'.format(str(f_default_print)), fg='green')
),
default = f_default,
show_default = False
)
# Only save if we've changed the default
if f_user != f_default:
# Convert string bools to real bools
Expand All @@ -85,14 +105,13 @@ def prompt_vars(self, params = None, direct = False):
except AttributeError:
pass
self.nxf_flags[flag] = f_user

# Uses the parameter values from the JSON file
# and does not ask the user to set them explicitly
if direct:
return

# Pipeline params
logging.info("Pipeline specific parameters:\n")
if params:
Launch.__prompt_defaults_from_param_objects(
Launch.__group_parameters(params)
Expand Down Expand Up @@ -143,39 +162,69 @@ def __prompt_defaults_from_param_objects(cls, params_grouped):
}
"""
for group_label, params in params_grouped.items():
print("{prespace}Parameter group: \'{label}\'{postspace}".format(
prespace='-'*5,
label=group_label,
postspace='-'*10)
)
use_defaults = click.confirm("Do you want to use the group's defaults?",
default=True)
if use_defaults:
click.echo("\n\n{}{}".format(
click.style('Parameter group: ', bold=True, underline=True),
click.style(group_label, bold=True, underline=True, fg='red'),
))
use_defaults = click.confirm(
"Do you want to change the group's defaults? "+click.style('[y/N]', fg='green'),
default=False, show_default=False)
if not use_defaults:
continue
for parameter in params:
value_is_valid = False
while(not value_is_valid):
desired_param_value = click.prompt("'--{name}'\n"
"\tUsage: {usage}\n"
"\tRange/Choices: {choices}.\n"
.format(name=parameter.name,
usage=parameter.usage,
choices=parameter.choices),
default=parameter.default_value)
first_attempt = True
while not value_is_valid:
# Start building the string to show to the user - label and usage
plines = ['',
click.style(parameter.label, bold=True),
click.style(parameter.usage, dim=True)
]
# Add the choices / range if applicable
if parameter.choices:
rc = 'Choices' if parameter.type == 'string' else 'Range'
plines.append('{}: {}'.format(rc, str(parameter.choices)))

# Reset the choice display if boolean
if parameter.type == "boolean":
pdef_val = 'Y/n' if parameter.default_value else 'y/N'
else:
pdef_val = parameter.default_value

# Final line to print - command and default
flag_prompt = click.style(' --{} '.format(parameter.name), fg='blue') + \
click.style('[{}]'.format(pdef_val), fg='green')
# Only show this final prompt if we're trying again
if first_attempt:
plines.append(flag_prompt)
else:
plines = [flag_prompt]
first_attempt = False

# Use click.confirm if a boolean for default input handling
if parameter.type == "boolean":
parameter.value = click.confirm("\n".join(plines),
default=parameter.default_value, show_default=False)
# Use click.prompt if anything else
else:
parameter.value = click.prompt("\n".join(plines),
default=parameter.default_value, show_default=False)

# Set input parameter types
if parameter.type == "integer":
desired_param_value = int(desired_param_value)
elif parameter.type == "boolean":
desired_param_value = (str(desired_param_value).lower() in ['yes', 'y', 'true', 't', '1'])
parameter.value = int(parameter.value)
elif parameter.type == "decimal":
desired_param_value = float(desired_param_value)
parameter.value = desired_param_value
parameter.value = float(parameter.value)

# Validate the input
try:
parameter.validate()
except Exception as e:
print(e)
click.secho("\nERROR: {}".format(e), fg='red')
click.secho("Please try again:")
continue
else:
value_is_valid = True
value_is_valid = True

def build_command(self, params = None):
""" Build the nextflow run command based on what we know """
Expand All @@ -189,13 +238,13 @@ def build_command(self, params = None):
# String values
else:
self.nextflow_cmd = '{} {} "{}"'.format(self.nextflow_cmd, flag, val.replace('"', '\\"'))

if params: # When a parameter specification file was used, we can run Nextflow with it
path = Launch.__create_nfx_params_file(params)
self.nextflow_cmd = '{} {} "{}"'.format(self.nextflow_cmd, "--params-file", path)
Launch.__write_params_as_full_json(params)
return

for param, val in self.params.items():
# Boolean flags like --saveTrimmed
if isinstance(val, bool):
Expand All @@ -215,7 +264,7 @@ def __create_nfx_params_file(cls, params):
with open(output_file, "w") as fp:
fp.write(json_string)
return output_file

@classmethod
def __write_params_as_full_json(cls, params, outdir = os.getcwd()):
output_file = os.path.join(outdir, "full-params.json")
Expand All @@ -226,7 +275,13 @@ def __write_params_as_full_json(cls, params, outdir = os.getcwd()):

def launch_workflow(self):
""" Launch nextflow if required """
logging.info("Nextflow command:\n {}\n\n".format(self.nextflow_cmd))
if click.confirm('Do you want to run this command now?'):
logging.info("Launching!")
click.secho("\n\nNextflow command:", bold=True, underline=True)
click.secho(" {}\n\n".format(self.nextflow_cmd), fg='magenta')

if click.confirm(
'Do you want to run this command now? '+click.style('[y/N]', fg='green'),
default=False,
show_default=False
):
logging.info("Launching workflow!")
subprocess.call(self.nextflow_cmd, shell=True)
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