# Copyright 2011-2014 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import argparse
import sys
import os
import imp
import io
FASTR_LOG_TYPE = 'none' # Do not get info about fastr
import fastr
from fastr.core.tool import Tool
from fastr.core.version import Version
from fastr.utils.cmd import add_parser_doc_link
[docs]def get_parser():
parser = argparse.ArgumentParser(
description="Extract basic information from argparse."
)
parser.add_argument('infile', metavar='SCRIPT.py', help='Python script to inspect')
parser.add_argument('outfile', metavar='TOOL.xml', help='created Tool stub')
return parser
[docs]def cardinality_from_nargs(value):
val_mapping = {'+': '1-*',
'?': '0-1',
'*': '0-*',
None: 1}
if isinstance(value, int):
return value
else:
return val_mapping[value]
[docs]def datatype_from_type(type_, metavar):
type_mapping = {int: 'Int',
float: 'Float',
bool: 'Boolean',
str: 'String',
None: 'String'}
if type_ in (None, str) and isinstance(metavar, str):
return fastr.types.guess_type(metavar.lower(), exists=False).id
else:
if type_ in (None, str) and metavar is not None:
type_ = type(metavar)
return type_mapping.get(type_, 'AnyType')
[docs]def main():
"""
Create a stub for a Tool based on a python script using argparse
"""
# No arguments were parsed yet, parse them now
parser = add_parser_doc_link(get_parser(), __file__)
args = parser.parse_args()
# Extract arguments
filepath = args.infile
output_path = args.outfile
# Extract argparse from desired script
parser, stdout = extract_argparser(filepath)
parser.prog = os.path.basename(filepath)
description = parser.description
if description is None:
description = 'auto generated tool from {}'.format(filepath)
tool = Tool()
tool.id = os.path.splitext(os.path.basename(filepath))[0]
tool.name = tool.id
tool.version = Version('1.0')
tool.filename = output_path
tool.node_class = 'NodeRun'
tool.command = {'authors': [],
'description': description,
'targets': [{'os': '*',
'arch': '*',
'bin': os.path.basename(filepath),
'interpreter': 'python',
'location': fastr.vfs.path_to_url(os.path.dirname(filepath)),
'module': None}],
'url': 'http://www.bigr.nl/fastr',
'version': Version('1.0'),
'license': 'UNKNOWN'}
tool.help = parser.format_help()
tool.authors = [{'name': 'extract_argparse.py',
'email': 'jsmith@example.org',
'url': 'http://example.org'}]
tool.description = description
tool.tests = []
inputs = []
for option in parser._optionals._group_actions:
prefix = max(option.option_strings, key=len)
id_ = prefix.strip('-')
param = {'id': id_,
'name': id_,
'prefix': prefix,
'description': option.help,
'cardinality': cardinality_from_nargs(option.nargs),
'required': option.required,
'repeat_prefix': False}
if option.const is not None:
param['datatype'] = datatype_from_type(option.type, option.const)
elif option.choices is not None:
param['enum'] = [str(x) for x in option.choices]
else:
param['datatype'] = datatype_from_type(option.type, option.metavar)
inputs.append(param)
tool.interface = fastr.plugins.FastrInterface(id_='{}_{}_interface'.format(tool.id, tool.command_version),
document={
'inputs': inputs,
'outputs': [],
})
if os.path.isdir(output_path):
output_path = os.path.join(output_path,
tool.id + '.xml')
with open(output_path, 'w') as output_fh:
output_fh.write(tool.dumps('xml'))
print('Written Tool stub to {}...'.format(output_path))
[docs]def find_argparser(entry, basename=sys.argv[0]):
# Catch stdout to string (no auto-print)
old_stdout = sys.stdout
temp_buffer = io.StringIO()
sys.stdout = temp_buffer
try:
# Call entry with --help to trigger help and SystemExit by argparse
sys.argv = [basename, '--help']
entry()
except SystemExit:
# Follow traceback frames until we find the first ArgumentParser object
tb = sys.exc_info()[2]
tb_stack = [tb]
while tb.tb_next is not None:
tb = tb.tb_next
tb_stack.append(tb)
for tb in tb_stack:
for name, obj in tb.tb_frame.f_locals.items():
if isinstance(obj, argparse.ArgumentParser):
return obj, temp_buffer.getvalue()
raise
finally:
# Cleanup StringIO and reset stdout
sys.stdout = old_stdout
temp_buffer.close()
if __name__ == '__main__':
main()