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"""Run docopt in GOATOOLS.""" |
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from __future__ import print_function |
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__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved." |
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__author__ = "DV Klopfenstein" |
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import sys |
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import re |
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from docopt import docopt |
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from goatools.gosubdag.utils import get_kwargs |
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class DocOptParse(object): |
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"""Run docopt in GOATOOLS.""" |
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def __init__(self, doc, exp_keys, exp_elems): |
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self.doc = doc |
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self.exp_keys = exp_keys if exp_keys else set() # Expected dictionary keys |
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self.exp_elems = exp_elems if exp_elems else set() # Expected set elements (True/False) |
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def get_docargs(self, args=None, prt=None, **kws): |
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"""Pare down docopt. Return a minimal dictionary and a set containing runtime arg values.""" |
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args_user = sys.argv[1:] if args is None else args |
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arg_kws = self._get_docargs(args_user, prt) |
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if 'intvals' in kws: |
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self._set_intvals(arg_kws, kws['intvals']) |
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return arg_kws |
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def _get_docargs(self, args_user, prt): |
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"""Pare down docopt. Return a minimal dictionary and a set containing runtime arg values.""" |
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if prt is not None: |
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print("DocOptParse BEFORE docopt: {}".format(args_user)) |
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docargs = docopt(self.doc, args_user) |
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if prt is not None: |
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print("DocOptParse AFTER docopt: {}".format(docargs)) |
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kwargs_doc = {re.sub(r'^-{1,2}', '', k):v for k, v in docargs.items()} |
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self._chk_docopt_kws(kwargs_doc, args_user) |
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kwargs_usr = get_kwargs(kwargs_doc, self.exp_keys, self.exp_elems) |
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if prt is not None: |
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print("DocOptParse AFTER pared: {}".format(kwargs_usr)) |
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for key in ['taxid']: |
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if key in kwargs_usr: |
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kwargs_usr[key] = int(kwargs_usr[key]) |
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if prt is not None: |
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print("DocOptParse AFTER edited/checked: {}".format(kwargs_usr)) |
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return kwargs_usr |
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@staticmethod |
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def _set_intvals(kws, keys): |
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"""Convert keyword values to int.""" |
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for key in keys: |
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if key in kws: |
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kws[key] = int(kws[key]) |
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def _chk_docopt_exit(self, args, exp_letters): |
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"""Check if docopt exit was for an unknown argument.""" |
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if args is None: |
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args = sys.argv[1:] |
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keys_all = self.exp_keys.union(self.exp_elems) |
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if exp_letters: |
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keys_all |= exp_letters |
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unknown_args = self._chk_docunknown(args, keys_all) |
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if unknown_args: |
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raise RuntimeError("{USAGE}\n **FATAL: UNKNOWN ARGS: {UNK}".format( |
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USAGE=self.doc, UNK=" ".join(unknown_args))) |
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def _chk_docopt_kws(self, docdict, exp): |
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"""Check for common user errors when running from the command-line.""" |
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for key, val in docdict.items(): |
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if isinstance(val, str): |
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assert '=' not in val, self._err("'=' FOUND IN VALUE", key, val, exp) |
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elif key != 'help' and key not in self.exp_keys and key not in self.exp_elems: |
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raise RuntimeError(self._err("UNKNOWN KEY", key, val, exp)) |
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def _err(self, msg, key, val, exp): |
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return "{DOC}\n{MSG}: KEY({K}) VAL({V}): {EXP}".format( |
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DOC=self.doc, MSG=msg, K=key, V=val, EXP=" ".join(exp)) |
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@staticmethod |
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def _chk_docunknown(args, exp): |
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"""Return any unknown args.""" |
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unknown = [] |
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for arg in args: |
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if arg[:2] == '--': |
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val = arg[2:] |
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if val not in exp: |
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unknown.append(arg) |
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elif arg[:1] == '-': |
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val = arg[1:] |
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if val not in exp: |
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unknown.append(arg) |
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if '-h' in unknown or '--help' in unknown: |
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return [] |
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return unknown |
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# Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved. |
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tanghaibao /
goatools
