hansel.Crumb._is_crumb_arg() - Code Metrics - Inspection of "Merge branch 'master' of github.com:alexsavio/hans..." - alexsavio/hansel - Measure and Improve Code Quality continuously with Scrutinizer

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by Alexandre M.

created 2015-12-30 19:50 UTC

hansel.Crumb._is_crumb_arg() A

↳ Parent: hansel.Crumb

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Metric	Value
cc	2
dl	0
loc	17
rs	9.4286

# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Crumb class: the smart path model class.
"""

import os
import os.path     as op
from   copy        import deepcopy
from   collections import OrderedDict, Mapping, Sequence
from   pathlib     import Path

from   six import string_types

from   hansel.utils import remove_duplicates, list_children


class Crumb(object):
    """ The crumb path model class.
    Parameters
    ----------
    crumb_path: str
        A file or folder path with crumb arguments. See Examples.

    Examples
    --------
    >>> crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")
    >>> cr = Crumb(op.join(op.expanduser('~'), '{user_folder}'))
    """
    _arg_start_sym = '{'
    _arg_end_sym   = '}'

    def __init__(self, crumb_path):
        self._path   = self._get_path(crumb_path)
        self._argidx = OrderedDict()
        self._update()

    @property
    def path(self):
        """Return the current crumb path string."""
        return self._path

    @path.setter
    def path(self, value):
        """ Set the current crumb path string and updates the internal members.
        Parameters
        ----------
        value: str
            A file or folder path with crumb arguments. See Examples in class docstring.
        """
        self._path = value
        self._update()

    def _check(self):
        if not self.is_valid(self._path):
            raise ValueError("The current crumb path has errors, got {}.".format(self.path))

    def _update(self):
        """ Clean up, parse the current crumb path and fill the internal
        members for functioning."""
        self._clean()
        self._check()
        self._set_argidx()
        self._set_replace_func()

    def _clean(self):
        """ Clean up the private utility members, i.e., _argidx. """
        self._argidx = OrderedDict()

    @classmethod
    def _arg_name(cls, arg):
        """ Return the name of the argument given its crumb representation.
        Parameters
        ----------
        arg_crumb: str

        Returns
        -------
        arg_name: str
        """
        if not cls._is_crumb_arg(arg):
            raise ValueError("Expected an well formed crumb argument, "
                             "got {}.".format(arg))
        return arg[1:-1]

    def _arg_format(self, arg_name):
        """ Return the argument for its string `format()` representation.
        Parameters
        ----------
        arg_name: str

        Returns
        -------
        arg_format: str
        """
        return '{' + arg_name + '}'

    def __eq__(self, other):
        """ Return True if `self` and `other` are equal, False otherwise.
        Parameters
        ----------
        other: Crumb

        Returns
        -------
        is_equal: bool
        """
        if self._path != other._path:
            return False

        if self._argidx != other._argidx:
            return False

        return True

    @classmethod
    def copy(cls, crumb):
        """ Return a deep copy of the given `crumb`.
        Parameters
        ----------
        crumb: str or Crumb

        Returns
        -------
        copy: Crumb
        """
        if isinstance(crumb, cls):
            return cls(crumb._path)
        elif isinstance(crumb, string_types):
            return cls.from_path(crumb)
        else:
            raise TypeError("Expected a Crumb or a str to copy, got {}.".format(type(crumb)))

    def _set_argidx(self):
        """ Initialize the self._argidx dict. It holds arg_name -> index.
        The index is the position in the whole `_path.split(op.sep)` where each argument is.
        """
        fs = self._path_split()
        for idx, f in enumerate(fs):
            if self._is_crumb_arg(f):
                self._argidx[self._arg_name(f)] = idx

    def _set_replace_func(self):
        """ Set the fastest replace algorithm depending on how
        many arguments the path has."""
        self._replace = self._replace2
        if len(self._argidx) > 5:
            self._replace = self._replace1

    def _find_arg(self, arg_name):
        """ Return the index in the current path of the crumb
        argument with name `arg_name`.
        """
        return self._argidx.get(arg_name, -1)

    def isabs(self):
        """ Return True if the current crumb path has an
        absolute path, False otherwise.
        This means that if it is valid and does not start with a `op.sep` character
        or hard disk letter.
        """
        if not self.is_valid(self._path):
            raise ValueError("The given crumb path has errors, got {}.".format(self.path))

        subp = self._path.split(self._arg_start_sym)[0]
        return op.isabs(subp)

    def abspath(self, first_is_basedir=False):
        """ Return a copy of `self` with an absolute crumb path.
        Add as prefix the absolute path to the current directory if the current
        crumb is not absolute.
        Parameters
        ----------
        first_is_basedir: bool
            If True and the current crumb path starts with a crumb argument and first_is_basedir,
            the first argument will be replaced by the absolute path to the current dir,
            otherwise the absolute path to the current dir will be added as a prefix.


        Returns
        -------
        abs_crumb: Crumb
        """
        if not self.is_valid(self._path):
            raise ValueError("The given crumb path has errors, got {}.".format(self.path))

        if self.isabs():
            return deepcopy(self)

        return self.copy(self._abspath(first_is_basedir=first_is_basedir))

    def _path_split(self):
        return self._path.split(op.sep)

    def _abspath(self, first_is_basedir=False):
        """ Return the absolute path of the current crumb path.
        Parameters
        ----------
        first_is_basedir: bool
            If True and the current crumb path starts with a crumb argument and first_is_basedir,
            the first argument will be replaced by the absolute path to the current dir,
            otherwise the absolute path to the current dir will be added as a prefix.


        Returns
        -------
        abspath: str
        """
        if not self.has_crumbs(self._path):
             return op.abspath(self._path)

        splt = self._path_split()
        path = []
        if self._is_crumb_arg(splt[0]):
            path.append(op.abspath(op.curdir))

        if not first_is_basedir:
            path.append(splt[0])

        if splt[1:]:
            path.extend(splt[1:])

        return op.sep.join(path)

    def split(self):
        """ Return a list of sub-strings of the current crumb path where the
            path parts are separated from the crumb arguments.

        Returns
        -------
        crumbs: list of str
        """
        return self._split(self._path)

    def _default_map(self):
        """ Return the dict with the default format values of the
            crumb arguments."""
        return {v: self._arg_format(v) for v in self._argidx}

    @classmethod
    def _split(cls, crumb_path):
        """ Return a list of sub-strings of `crumb_path` where the
            path parts are separated from the crumb arguments.
        """
        crumb_path = cls._get_path(crumb_path)

        splt = []
        tmp = '/' if crumb_path.startswith(op.sep) else ''
        for i in crumb_path.split(op.sep):
            if i.startswith(cls._arg_start_sym):
                splt.append(tmp)
                tmp = ''
                splt.append(i)
            else:
                tmp = op.join(tmp, i)

        return splt

    @classmethod
    def is_valid(cls, crumb_path):
        """ Return True if `crumb_path` is a well formed path with crumb arguments,
        False otherwise.
        Parameters
        ----------
        crumb_path: str

        Returns
        -------
        is_valid: bool
        """
        crumb_path = cls._get_path(crumb_path)

        splt = crumb_path.split(op.sep)
        for crumb in splt:
            if op.isdir(crumb):
                continue

            if cls._is_crumb_arg(crumb):
                crumb = cls._arg_name(crumb)

            if cls._arg_start_sym in crumb or cls._arg_end_sym in crumb:
                return False

        return True

    @classmethod
    def _is_crumb_arg(cls, crumb_arg):
        """ Returns True if `crumb_arg` is a well formed
        crumb argument.
        Parameters
        ----------
        crumb_arg: str
            The string representing a crumb argument, e.g., "{sample_id}"

        Returns
        -------
        is_crumb_arg: bool
        """
        if not isinstance(crumb_arg, string_types):
            return False

        return crumb_arg.startswith(cls._arg_start_sym) and crumb_arg.endswith(cls._arg_end_sym)

    @classmethod
    def has_crumbs(cls, crumb_path):
        """ Return True if the `crumb_path.split(op.sep)` has item which is a crumb argument
        that starts with '{' and ends with '}'."""
        crumb_path = cls._get_path(crumb_path)

        splt = crumb_path.split(op.sep)
        for i in splt:
            if cls._is_crumb_arg(i):
                return True

        return False

    @classmethod
    def _get_path(cls, crumb_path):
        """ Return the path string from `crumb_path`.
        Parameters
        ----------
        crumb_path: str or Crumb

        Returns
        -------
        path: str
        """
        if isinstance(crumb_path, cls):
            crumb_path = crumb_path._path

        if not isinstance(crumb_path, string_types):
            raise TypeError("Expected `crumb_path` to be a {}, got {}.".format(string_types, type(crumb_path)))

        return crumb_path

    @classmethod
    def from_path(cls, crumb_path):
        """ Create an instance of Crumb or pathlib.Path out of `crumb_path`.
        It will return a Crumb if `crumb_path` has crumbs or
        Parameters
        ----------
        val: str, Crumb or pathlib.Path

        Returns
        -------
        path: Crumb or pathlib.Path
        """
        if isinstance(crumb_path, (cls, Path)):
            return crumb_path

        if isinstance(crumb_path, string_types):
            if cls.has_crumbs(crumb_path):
                return cls(crumb_path)
            else:
                return Path(crumb_path)
        else:
            raise TypeError("Expected a `val` to be a `str`, got {}.".format(type(crumb_path)))

    def _replace1(self, **kwargs):
        if not kwargs:
            return self._path

        args = self._default_map()
        for k in kwargs:
            if k not in args:
                raise KeyError("Could not find argument {}"
                               " in `path` {}.".format(k, self._path))

            args[k] = kwargs[k]

        return self._path.format_map(args)

    def _replace2(self, **kwargs):
        if not kwargs:
            return self._path

        path = self._path
        for k in kwargs:
            karg = self._arg_format(k)
            if k not in path:
                raise KeyError("Could not find argument {} in"
                               " `path` {}.".format(k, self._path))

            path = path.replace(karg, kwargs[k])

        return path

    def _lastarg(self):
        """ Return the name and idx of the last argument."""
        for arg, idx in reversed(list(self._argidx.items())):
            return arg, idx

    def _firstarg(self):
        """ Return the name and idx of the first argument."""
        for arg, idx in self._argidx.items():
            return arg, idx

    def _is_firstarg(self, arg_name):
        """ Return True if `arg_name` is the first argument."""
        # Take into account that self._argidx is OrderedDict
        return arg_name == self._firstarg()[0]

    def _arg_values(self, arg_name, arg_values=None):
        """ Return the existing values in the file system for the crumb argument
        with name `arg_name`.
        The `arg_values` must be a sequence with the tuples with valid values of the dependent
        (previous in the path) crumb arguments.
        The format of `arg_values` work in such a way that `self._path.format(dict(arg_values[0]))`
        would give me a valid path or crumb.
        Parameters
        ----------
        arg_name: str

        arg_values: list of tuples

        Returns
        -------
        vals: list of tuples

        Raises
        ------
        ValueError: if `arg_values` is None and `arg_name` is not the
        first crumb argument in self._path

        IOError: if this crosses to any path that is non-existing.
        """
        if arg_values is None and not self._is_firstarg(arg_name):
            raise ValueError("Cannot get the list of values for {} if"
                             " the previous arguments are not filled"
                             " in `paths`.".format(arg_name))

        aidx = self._find_arg(arg_name)

        # check if the path is absolute, do it absolute
        apath = self._abspath()
        splt = apath.split(op.sep)

        if aidx == len(splt) - 1:  # this means we have to list files too
            just_dirs = False
        else:  # this means we have to list folders
            just_dirs = True

        vals = []
        if arg_values is None:
            base = op.sep.join(splt[:aidx])
            vals = [[(arg_name, val)] for val in list_children(base, just_dirs=just_dirs)]
        else:
            for aval in arg_values:
                #  create the part of the crumb path that is already specified
                path = self._split(self._replace(**dict(aval)))[0]

                #  list the children of `path`
                subpaths = list_children(path, just_dirs=just_dirs)

                #  extend `val` tuples with the new list of values for `aval`
                vals.extend([aval + [(arg_name, sp)] for sp in subpaths])

        return vals

    def replace(self, **kwargs):
        """ Return a copy of self with the crumb arguments in
        `kwargs` replaced by its values.
        Parameters
        ----------
        kwargs: strings

        Returns
        -------
        crumb:
        """
        for arg_name in kwargs:
            if arg_name not in self._argidx:
                raise KeyError("Expected `arg_name` to be one of ({}),"
                                 " got {}.".format(list(self._argidx), arg_name))

        cr = self.copy(self)
        cr._path = cr._replace(**kwargs)
        return Crumb.from_path(cr._path)

    def _arg_deps(self, arg_name):
        """ Return a subdict of `self._argidx` with the
         values from the crumb arguments that come before
         `arg_name` in the crumb path.
        Parameters
        ----------
        arg_name: str

        Returns
        -------
        arg_deps: Mapping[str, int]
        """
        argidx = self._find_arg(arg_name)
        return OrderedDict([(arg, idx) for arg, idx in self._argidx.items() if idx <= argidx])

    def ls(self, arg_name, fullpath=True, duplicates=True, make_crumbs=True, check_exists=False):
        """
        Return the list of values for the argument crumb `arg_name`.
        This will also unfold any other argument crumb that appears before in the
        path.
        Parameters
        ----------
        arg_name: str
            Name of the argument crumb to be unfolded.

        fullpath: bool
            If True will build the full path of the crumb path, will also append
            the rest of crumbs not unfolded.
            If False will only return the values for the argument with name
            `arg_name`.

        duplicates: bool
            If False will remove and sort the duplicate values from the result.
            Otherwise it will leave it as it is.

        make_crumbs: bool
            If `fullpath` and `make_crumbs` is True will create a Crumb or a pathlib.Path
            for each element of the result. This will depende if the result item still has
            crumb arguments or not.

        check_exists: bool
            If True will return only str, Crumb or Path if it exists
            in the file path, otherwise it may create file paths
            that don't have to exist.

        Returns
        -------
        values: list of str or Crumb

        Examples
        --------
        >>> cr = Crumb(op.join(op.expanduser('~'), '{user_folder}'))
        >>> user_folders = cr.ls('user_folder', fullpath=True, duplicates=True, make_crumbs=True)
        """
        if arg_name not in self._argidx:
            raise ValueError("Expected `arg_name` to be one of ({}),"
                             " got {}.".format(list(self._argidx), arg_name))

        # if the first chunk of the path is a parameter, I am not interested in this (for now)
        if self._path.startswith(self._arg_start_sym):
            raise NotImplementedError("Can't list paths that starts"
                                      " with an argument.")

        if make_crumbs and not fullpath:
            raise ValueError("`make_crumbs` can only work if `fullpath` is also True.")

        arg_deps = self._arg_deps(arg_name)
        values_map = None
        for arg in arg_deps:
            values_map = self._arg_values(arg, values_map)

        if check_exists:
            return self._ls_check_exists(arg_name, values_map=values_map,
                                         fullpath=fullpath,
                                         duplicates=duplicates,
                                         make_crumbs=make_crumbs)
        else:
            return self._ls_no_check_exists(arg_name, values_map=values_map,
                                            fullpath=fullpath,
                                            duplicates=duplicates,
                                            make_crumbs=make_crumbs)

    def _ls_no_check_exists(self, arg_name, values_map, fullpath, duplicates, make_crumbs):
        if not fullpath:  # this means we can return the list of crumbs directly
            values = [dict(val)[arg_name] for val in values_map]
        else:  # this means we have to build the full paths
            values = [self._replace(**dict(val)) for val in values_map]

        if not duplicates:
            values = remove_duplicates(values)

        if fullpath and make_crumbs:
            values = [self.from_path(val) for val in values]

        return values

    def _ls_check_exists(self, arg_name, values_map, fullpath, duplicates, make_crumbs):

        paths = [self._replace(**dict(val)) for val in values_map]
        paths = [self.from_path(val) for val in paths]
        paths = [val for val in paths if val.exists()]

        if not fullpath:
            argidx = self._argidx[arg_name]
            values = [str(val).split(op.sep)[argidx] for val in paths]
        else:
            if make_crumbs:
                values = paths
            else:
                values = [str(val) for val in paths]

        return values

    def _remaining_deps(self, arg_names):
        """ Return the name of the arguments that are dependencies of `arg_names`.
        Parameters
        ----------
        arg_names: Sequence[str]

        Returns
        -------
        rem_deps: Sequence[str]
        """
        started = False
        rem_deps = []
        for an in reversed(list(self._argidx.keys())):  # take into account that argidx is ordered
            if an in arg_names:
                started = True
            else:
                if started:
                    rem_deps.append(an)

        return rem_deps

    def touch(self):
        """ Create a leaf directory and all intermediate ones
        using the non crumbed part of `crumb_path`.
        If the target directory already exists, raise an IOError
        if exist_ok is False. Otherwise no exception is raised.
        Parameters
        ----------
        crumb_path: str

        exist_ok: bool
            Default = True

        Returns
        -------
        nupath: str
            The new path created.
        """
        return self._touch(self._path)

    @classmethod
    def _touch(cls, crumb_path, exist_ok=True):
        """ Create a leaf directory and all intermediate ones
        using the non crumbed part of `crumb_path`.
        If the target directory already exists, raise an IOError
        if exist_ok is False. Otherwise no exception is raised.
        Parameters
        ----------
        crumb_path: str

        exist_ok: bool
            Default = True

        Returns
        -------
        nupath: str
            The new path created.
        """
        if cls.has_crumbs(crumb_path):
            nupath = cls._split(crumb_path)[0]
        else:
            nupath = crumb_path

        if op.exists(nupath) and not exist_ok:
            raise IOError("Folder {} already exists.".format(nupath))

        try:
            os.makedirs(nupath, exist_ok=exist_ok)
        except:
            raise
        else:
            return nupath

    def exists(self):
        """ Return True if the current crumb path is a possibly existing path,
        False otherwise.
        Returns
        -------
        exists: bool
        """
        if not op.exists(self.split()[0]):
            return False

        last, _ = self._lastarg()
        paths = self.ls(last,
                        fullpath     = True,
                        make_crumbs  = False,
                        duplicates   = True,
                        check_exists = False)

        return all([self._split_exists(lp) for lp in paths])

    def has_files(self):
        """ Return True if the current crumb path has any file in its
        possible paths.
        Returns
        -------
        has_files: bool
        """
        if not op.exists(self.split()[0]):
            return False

        last, _ = self._lastarg()
        paths = self.ls(last,
                        fullpath     = True,
                        make_crumbs  = True,
                        duplicates   = True,
                        check_exists = True)

        return any([op.isfile(str(lp)) for lp in paths])

    def unfold(self):
        """ Return a list of all the existing paths until the last crumb argument.
        Returns
        -------
        paths: list of pathlib.Path
        """
        return self.ls(self._lastarg()[0],
                       fullpath    = True,
                       duplicates  = False,
                       make_crumbs = True,
                       check_exists= True)

    @classmethod
    def _split_exists(cls, crumb_path):
        """ Return True if the part without crumb arguments of `crumb_path`
        is an existing path or a symlink, False otherwise.
        Returns
        -------
        exists: bool
        """
        if cls.has_crumbs(crumb_path):
            rpath = cls._split(crumb_path)[0]
        else:
            rpath = str(crumb_path)

        return op.exists(rpath) or op.islink(rpath)

    def __getitem__(self, item):
        return self.ls(item,
                       fullpath    = False,
                       duplicates  = False,
                       make_crumbs = False,
                       check_exists= True)

    def __setitem__(self, key, value):
        if key not in self._argidx:
            raise KeyError("Expected `arg_name` to be one of ({}),"
                           " got {}.".format(list(self._argidx), key))

        self._path = self._replace(**{key: value})
        self._update()

    def __contains__(self, item):
        return item in self._argidx

    def __repr__(self):
        return '{}("{}")'.format(__class__.__name__, self._path)

    def __str__(self):
        return str(self._path)




1			# -- coding: utf-8 --
2			# emacs: -- mode: python; py-indent-offset: 4; indent-tabs-mode: nil --
3			# vi: set ft=python sts=4 ts=4 sw=4 et:
4			"""
5			Crumb class: the smart path model class.
6			"""
7
8			import os
9			import os.path as op
10			from copy import deepcopy
11			from collections import OrderedDict, Mapping, Sequence
12			from pathlib import Path
13
14			from six import string_types
15
16			from hansel.utils import remove_duplicates, list_children
17
18
19			class Crumb(object):
20			""" The crumb path model class.
21			Parameters
22			----------
23			crumb_path: str
24			A file or folder path with crumb arguments. See Examples.
25
26			Examples
27			--------
28			>>> crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")
29			>>> cr = Crumb(op.join(op.expanduser('~'), '{user_folder}'))
30			"""
31			_arg_start_sym = '{'
32			_arg_end_sym = '}'
33
34			def __init__(self, crumb_path):
35			self._path = self._get_path(crumb_path)
36			self._argidx = OrderedDict()
37			self._update()
38
39			@property
40			def path(self):
41			"""Return the current crumb path string."""
42			return self._path
43
44			@path.setter
45			def path(self, value):
46			""" Set the current crumb path string and updates the internal members.
47			Parameters
48			----------
49			value: str
50			A file or folder path with crumb arguments. See Examples in class docstring.
51			"""
52			self._path = value
53			self._update()
54
55			def _check(self):
56			if not self.is_valid(self._path):
57			raise ValueError("The current crumb path has errors, got {}.".format(self.path))
58
59			def _update(self):
60			""" Clean up, parse the current crumb path and fill the internal
61			members for functioning."""
62			self._clean()
63			self._check()
64			self._set_argidx()
65			self._set_replace_func()
66
67			def _clean(self):
68			""" Clean up the private utility members, i.e., _argidx. """
69			self._argidx = OrderedDict()
70
71			@classmethod
72			def _arg_name(cls, arg):
73			""" Return the name of the argument given its crumb representation.
74			Parameters
75			----------
76			arg_crumb: str
77
78			Returns
79			-------
80			arg_name: str
81			"""
82			if not cls._is_crumb_arg(arg):
83			raise ValueError("Expected an well formed crumb argument, "
84			"got {}.".format(arg))
85			return arg[1:-1]
86
87			def _arg_format(self, arg_name):
88			""" Return the argument for its string `format()` representation.
89			Parameters
90			----------
91			arg_name: str
92
93			Returns
94			-------
95			arg_format: str
96			"""
97			return '{' + arg_name + '}'
98
99			def __eq__(self, other):
100			""" Return True if `self` and `other` are equal, False otherwise.
101			Parameters
102			----------
103			other: Crumb
104
105			Returns
106			-------
107			is_equal: bool
108			"""
109			if self._path != other._path:
110			return False
111
112			if self._argidx != other._argidx:
113			return False
114
115			return True
116
117			@classmethod
118			def copy(cls, crumb):
119			""" Return a deep copy of the given `crumb`.
120			Parameters
121			----------
122			crumb: str or Crumb
123
124			Returns
125			-------
126			copy: Crumb
127			"""
128			if isinstance(crumb, cls):
129			return cls(crumb._path)
130			elif isinstance(crumb, string_types):
131			return cls.from_path(crumb)
132			else:
133			raise TypeError("Expected a Crumb or a str to copy, got {}.".format(type(crumb)))
134
135			def _set_argidx(self):
136			""" Initialize the self._argidx dict. It holds arg_name -> index.
137			The index is the position in the whole `_path.split(op.sep)` where each argument is.
138			"""
139			fs = self._path_split()
140			for idx, f in enumerate(fs):
141			if self._is_crumb_arg(f):
142			self._argidx[self._arg_name(f)] = idx
143
144			def _set_replace_func(self):
145			""" Set the fastest replace algorithm depending on how
146			many arguments the path has."""
147			self._replace = self._replace2
148			if len(self._argidx) > 5:
149			self._replace = self._replace1
150
151			def _find_arg(self, arg_name):
152			""" Return the index in the current path of the crumb
153			argument with name `arg_name`.
154			"""
155			return self._argidx.get(arg_name, -1)
156
157			def isabs(self):
158			""" Return True if the current crumb path has an
159			absolute path, False otherwise.
160			This means that if it is valid and does not start with a `op.sep` character
161			or hard disk letter.
162			"""
163			if not self.is_valid(self._path):
164			raise ValueError("The given crumb path has errors, got {}.".format(self.path))
165
166			subp = self._path.split(self._arg_start_sym)[0]
167			return op.isabs(subp)
168
169			def abspath(self, first_is_basedir=False):
170			""" Return a copy of `self` with an absolute crumb path.
171			Add as prefix the absolute path to the current directory if the current
172			crumb is not absolute.
173			Parameters
174			----------
175			first_is_basedir: bool
176			If True and the current crumb path starts with a crumb argument and first_is_basedir,
177			the first argument will be replaced by the absolute path to the current dir,
178			otherwise the absolute path to the current dir will be added as a prefix.
179
180
181			Returns
182			-------
183			abs_crumb: Crumb
184			"""
185			if not self.is_valid(self._path):
186			raise ValueError("The given crumb path has errors, got {}.".format(self.path))
187
188			if self.isabs():
189			return deepcopy(self)
190
191			return self.copy(self._abspath(first_is_basedir=first_is_basedir))
192
193			def _path_split(self):
194			return self._path.split(op.sep)
195
196			def _abspath(self, first_is_basedir=False):
197			""" Return the absolute path of the current crumb path.
198			Parameters
199			----------
200			first_is_basedir: bool
201			If True and the current crumb path starts with a crumb argument and first_is_basedir,
202			the first argument will be replaced by the absolute path to the current dir,
203			otherwise the absolute path to the current dir will be added as a prefix.
204
205
206			Returns
207			-------
208			abspath: str
209			"""
210			if not self.has_crumbs(self._path):
211			return op.abspath(self._path)
212
213			splt = self._path_split()
214			path = []
215			if self._is_crumb_arg(splt[0]):
216			path.append(op.abspath(op.curdir))
217
218			if not first_is_basedir:
219			path.append(splt[0])
220
221			if splt[1:]:
222			path.extend(splt[1:])
223
224			return op.sep.join(path)
225
226			def split(self):
227			""" Return a list of sub-strings of the current crumb path where the
228			path parts are separated from the crumb arguments.
229
230			Returns
231			-------
232			crumbs: list of str
233			"""
234			return self._split(self._path)
235
236			def _default_map(self):
237			""" Return the dict with the default format values of the
238			crumb arguments."""
239			return {v: self._arg_format(v) for v in self._argidx}
240
241			@classmethod
242			def _split(cls, crumb_path):
243			""" Return a list of sub-strings of `crumb_path` where the
244			path parts are separated from the crumb arguments.
245			"""
246			crumb_path = cls._get_path(crumb_path)
247
248			splt = []
249			tmp = '/' if crumb_path.startswith(op.sep) else ''
250			for i in crumb_path.split(op.sep):
251			if i.startswith(cls._arg_start_sym):
252			splt.append(tmp)
253			tmp = ''
254			splt.append(i)
255			else:
256			tmp = op.join(tmp, i)
257
258			return splt
259
260			@classmethod
261			def is_valid(cls, crumb_path):
262			""" Return True if `crumb_path` is a well formed path with crumb arguments,
263			False otherwise.
264			Parameters
265			----------
266			crumb_path: str
267
268			Returns
269			-------
270			is_valid: bool
271			"""
272			crumb_path = cls._get_path(crumb_path)
273
274			splt = crumb_path.split(op.sep)
275			for crumb in splt:
276			if op.isdir(crumb):
277			continue
278
279			if cls._is_crumb_arg(crumb):
280			crumb = cls._arg_name(crumb)
281
282			if cls._arg_start_sym in crumb or cls._arg_end_sym in crumb:
283			return False
284
285			return True
286
287			@classmethod
288			def _is_crumb_arg(cls, crumb_arg):
289			""" Returns True if `crumb_arg` is a well formed
290			crumb argument.
291			Parameters
292			----------
293			crumb_arg: str
294			The string representing a crumb argument, e.g., "{sample_id}"
295
296			Returns
297			-------
298			is_crumb_arg: bool
299			"""
300			if not isinstance(crumb_arg, string_types):
301			return False
302
303			return crumb_arg.startswith(cls._arg_start_sym) and crumb_arg.endswith(cls._arg_end_sym)
304
305			@classmethod
306			def has_crumbs(cls, crumb_path):
307			""" Return True if the `crumb_path.split(op.sep)` has item which is a crumb argument
308			that starts with '{' and ends with '}'."""
309			crumb_path = cls._get_path(crumb_path)
310
311			splt = crumb_path.split(op.sep)
312			for i in splt:
313			if cls._is_crumb_arg(i):
314			return True
315
316			return False
317
318			@classmethod
319			def _get_path(cls, crumb_path):
320			""" Return the path string from `crumb_path`.
321			Parameters
322			----------
323			crumb_path: str or Crumb
324
325			Returns
326			-------
327			path: str
328			"""
329			if isinstance(crumb_path, cls):
330			crumb_path = crumb_path._path
331
332			if not isinstance(crumb_path, string_types):
333			raise TypeError("Expected `crumb_path` to be a {}, got {}.".format(string_types, type(crumb_path)))
334
335			return crumb_path
336
337			@classmethod
338			def from_path(cls, crumb_path):
339			""" Create an instance of Crumb or pathlib.Path out of `crumb_path`.
340			It will return a Crumb if `crumb_path` has crumbs or
341			Parameters
342			----------
343			val: str, Crumb or pathlib.Path
344
345			Returns
346			-------
347			path: Crumb or pathlib.Path
348			"""
349			if isinstance(crumb_path, (cls, Path)):
350			return crumb_path
351
352			if isinstance(crumb_path, string_types):
353			if cls.has_crumbs(crumb_path):
354			return cls(crumb_path)
355			else:
356			return Path(crumb_path)
357			else:
358			raise TypeError("Expected a `val` to be a `str`, got {}.".format(type(crumb_path)))
359
360			def _replace1(self, **kwargs):
361			if not kwargs:
362			return self._path
363
364			args = self._default_map()
365			for k in kwargs:
366			if k not in args:
367			raise KeyError("Could not find argument {}"
368			" in `path` {}.".format(k, self._path))
369
370			args[k] = kwargs[k]
371
372			return self._path.format_map(args)
373
374			def _replace2(self, **kwargs):
375			if not kwargs:
376			return self._path
377
378			path = self._path
379			for k in kwargs:
380			karg = self._arg_format(k)
381			if k not in path:
382			raise KeyError("Could not find argument {} in"
383			" `path` {}.".format(k, self._path))
384
385			path = path.replace(karg, kwargs[k])
386
387			return path
388
389			def _lastarg(self):
390			""" Return the name and idx of the last argument."""
391			for arg, idx in reversed(list(self._argidx.items())):
392			return arg, idx
393
394			def _firstarg(self):
395			""" Return the name and idx of the first argument."""
396			for arg, idx in self._argidx.items():
397			return arg, idx
398
399			def _is_firstarg(self, arg_name):
400			""" Return True if `arg_name` is the first argument."""
401			# Take into account that self._argidx is OrderedDict
402			return arg_name == self._firstarg()[0]
403
404			def _arg_values(self, arg_name, arg_values=None):
405			""" Return the existing values in the file system for the crumb argument
406			with name `arg_name`.
407			The `arg_values` must be a sequence with the tuples with valid values of the dependent
408			(previous in the path) crumb arguments.
409			The format of `arg_values` work in such a way that `self._path.format(dict(arg_values[0]))`
410			would give me a valid path or crumb.
411			Parameters
412			----------
413			arg_name: str
414
415			arg_values: list of tuples
416
417			Returns
418			-------
419			vals: list of tuples
420
421			Raises
422			------
423			ValueError: if `arg_values` is None and `arg_name` is not the
424			first crumb argument in self._path
425
426			IOError: if this crosses to any path that is non-existing.
427			"""
428			if arg_values is None and not self._is_firstarg(arg_name):
429			raise ValueError("Cannot get the list of values for {} if"
430			" the previous arguments are not filled"
431			" in `paths`.".format(arg_name))
432
433			aidx = self._find_arg(arg_name)
434
435			# check if the path is absolute, do it absolute
436			apath = self._abspath()
437			splt = apath.split(op.sep)
438
439			if aidx == len(splt) - 1: # this means we have to list files too
440			just_dirs = False
441			else: # this means we have to list folders
442			just_dirs = True
443
444			vals = []
445			if arg_values is None:
446			base = op.sep.join(splt[:aidx])
447			vals = [[(arg_name, val)] for val in list_children(base, just_dirs=just_dirs)]
448			else:
449			for aval in arg_values:
450			# create the part of the crumb path that is already specified
451			path = self._split(self._replace(**dict(aval)))[0]
452
453			# list the children of `path`
454			subpaths = list_children(path, just_dirs=just_dirs)
455
456			# extend `val` tuples with the new list of values for `aval`
457			vals.extend([aval + [(arg_name, sp)] for sp in subpaths])
458
459			return vals
460
461			def replace(self, **kwargs):
462			""" Return a copy of self with the crumb arguments in
463			`kwargs` replaced by its values.
464			Parameters
465			----------
466			kwargs: strings
467
468			Returns
469			-------
470			crumb:
471			"""
472			for arg_name in kwargs:
473			if arg_name not in self._argidx:
474			raise KeyError("Expected `arg_name` to be one of ({}),"
475			" got {}.".format(list(self._argidx), arg_name))
476
477			cr = self.copy(self)
478			cr._path = cr._replace(**kwargs)
479			return Crumb.from_path(cr._path)
480
481			def _arg_deps(self, arg_name):
482			""" Return a subdict of `self._argidx` with the
483			values from the crumb arguments that come before
484			`arg_name` in the crumb path.
485			Parameters
486			----------
487			arg_name: str
488
489			Returns
490			-------
491			arg_deps: Mapping[str, int]
492			"""
493			argidx = self._find_arg(arg_name)
494			return OrderedDict([(arg, idx) for arg, idx in self._argidx.items() if idx <= argidx])
495
496			def ls(self, arg_name, fullpath=True, duplicates=True, make_crumbs=True, check_exists=False):
497			"""
498			Return the list of values for the argument crumb `arg_name`.
499			This will also unfold any other argument crumb that appears before in the
500			path.
501			Parameters
502			----------
503			arg_name: str
504			Name of the argument crumb to be unfolded.
505
506			fullpath: bool
507			If True will build the full path of the crumb path, will also append
508			the rest of crumbs not unfolded.
509			If False will only return the values for the argument with name
510			`arg_name`.
511
512			duplicates: bool
513			If False will remove and sort the duplicate values from the result.
514			Otherwise it will leave it as it is.
515
516			make_crumbs: bool
517			If `fullpath` and `make_crumbs` is True will create a Crumb or a pathlib.Path
518			for each element of the result. This will depende if the result item still has
519			crumb arguments or not.
520
521			check_exists: bool
522			If True will return only str, Crumb or Path if it exists
523			in the file path, otherwise it may create file paths
524			that don't have to exist.
525
526			Returns
527			-------
528			values: list of str or Crumb
529
530			Examples
531			--------
532			>>> cr = Crumb(op.join(op.expanduser('~'), '{user_folder}'))
533			>>> user_folders = cr.ls('user_folder', fullpath=True, duplicates=True, make_crumbs=True)
534			"""
535			if arg_name not in self._argidx:
536			raise ValueError("Expected `arg_name` to be one of ({}),"
537			" got {}.".format(list(self._argidx), arg_name))
538
539			# if the first chunk of the path is a parameter, I am not interested in this (for now)
540			if self._path.startswith(self._arg_start_sym):
541			raise NotImplementedError("Can't list paths that starts"
542			" with an argument.")
543
544			if make_crumbs and not fullpath:
545			raise ValueError("`make_crumbs` can only work if `fullpath` is also True.")
546
547			arg_deps = self._arg_deps(arg_name)
548			values_map = None
549			for arg in arg_deps:
550			values_map = self._arg_values(arg, values_map)
551
552			if check_exists:
553			return self._ls_check_exists(arg_name, values_map=values_map,
554			fullpath=fullpath,
555			duplicates=duplicates,
556			make_crumbs=make_crumbs)
557			else:
558			return self._ls_no_check_exists(arg_name, values_map=values_map,
559			fullpath=fullpath,
560			duplicates=duplicates,
561			make_crumbs=make_crumbs)
562
563			def _ls_no_check_exists(self, arg_name, values_map, fullpath, duplicates, make_crumbs):
564			if not fullpath: # this means we can return the list of crumbs directly
565			values = [dict(val)[arg_name] for val in values_map]
566			else: # this means we have to build the full paths
567			values = [self._replace(**dict(val)) for val in values_map]
568
569			if not duplicates:
570			values = remove_duplicates(values)
571
572			if fullpath and make_crumbs:
573			values = [self.from_path(val) for val in values]
574
575			return values
576
577			def _ls_check_exists(self, arg_name, values_map, fullpath, duplicates, make_crumbs):
578
579			paths = [self._replace(**dict(val)) for val in values_map]
580			paths = [self.from_path(val) for val in paths]
581			paths = [val for val in paths if val.exists()]
582
583			if not fullpath:
584			argidx = self._argidx[arg_name]
585			values = [str(val).split(op.sep)[argidx] for val in paths]
586			else:
587			if make_crumbs:
588			values = paths
589			else:
590			values = [str(val) for val in paths]
591
592			return values
593
594			def _remaining_deps(self, arg_names):
595			""" Return the name of the arguments that are dependencies of `arg_names`.
596			Parameters
597			----------
598			arg_names: Sequence[str]
599
600			Returns
601			-------
602			rem_deps: Sequence[str]
603			"""
604			started = False
605			rem_deps = []
606			for an in reversed(list(self._argidx.keys())): # take into account that argidx is ordered
607			if an in arg_names:
608			started = True
609			else:
610			if started:
611			rem_deps.append(an)
612
613			return rem_deps
614
615			def touch(self):
616			""" Create a leaf directory and all intermediate ones
617			using the non crumbed part of `crumb_path`.
618			If the target directory already exists, raise an IOError
619			if exist_ok is False. Otherwise no exception is raised.
620			Parameters
621			----------
622			crumb_path: str
623
624			exist_ok: bool
625			Default = True
626
627			Returns
628			-------
629			nupath: str
630			The new path created.
631			"""
632			return self._touch(self._path)
633
634			@classmethod
635			def _touch(cls, crumb_path, exist_ok=True):
636			""" Create a leaf directory and all intermediate ones
637			using the non crumbed part of `crumb_path`.
638			If the target directory already exists, raise an IOError
639			if exist_ok is False. Otherwise no exception is raised.
640			Parameters
641			----------
642			crumb_path: str
643
644			exist_ok: bool
645			Default = True
646
647			Returns
648			-------
649			nupath: str
650			The new path created.
651			"""
652			if cls.has_crumbs(crumb_path):
653			nupath = cls._split(crumb_path)[0]
654			else:
655			nupath = crumb_path
656
657			if op.exists(nupath) and not exist_ok:
658			raise IOError("Folder {} already exists.".format(nupath))
659
660			try:
661			os.makedirs(nupath, exist_ok=exist_ok)
662			except:
663			raise
664			else:
665			return nupath
666
667			def exists(self):
668			""" Return True if the current crumb path is a possibly existing path,
669			False otherwise.
670			Returns
671			-------
672			exists: bool
673			"""
674			if not op.exists(self.split()[0]):
675			return False
676
677			last, _ = self._lastarg()
678			paths = self.ls(last,
679			fullpath = True,
680			make_crumbs = False,
681			duplicates = True,
682			check_exists = False)
683
684			return all([self._split_exists(lp) for lp in paths])
685
686			def has_files(self):
687			""" Return True if the current crumb path has any file in its
688			possible paths.
689			Returns
690			-------
691			has_files: bool
692			"""
693			if not op.exists(self.split()[0]):
694			return False
695
696			last, _ = self._lastarg()
697			paths = self.ls(last,
698			fullpath = True,
699			make_crumbs = True,
700			duplicates = True,
701			check_exists = True)
702
703			return any([op.isfile(str(lp)) for lp in paths])
704
705			def unfold(self):
706			""" Return a list of all the existing paths until the last crumb argument.
707			Returns
708			-------
709			paths: list of pathlib.Path
710			"""
711			return self.ls(self._lastarg()[0],
712			fullpath = True,
713			duplicates = False,
714			make_crumbs = True,
715			check_exists= True)
716
717			@classmethod
718			def _split_exists(cls, crumb_path):
719			""" Return True if the part without crumb arguments of `crumb_path`
720			is an existing path or a symlink, False otherwise.
721			Returns
722			-------
723			exists: bool
724			"""
725			if cls.has_crumbs(crumb_path):
726			rpath = cls._split(crumb_path)[0]
727			else:
728			rpath = str(crumb_path)
729
730			return op.exists(rpath) or op.islink(rpath)
731
732			def __getitem__(self, item):
733			return self.ls(item,
734			fullpath = False,
735			duplicates = False,
736			make_crumbs = False,
737			check_exists= True)
738
739			def __setitem__(self, key, value):
740			if key not in self._argidx:
741			raise KeyError("Expected `arg_name` to be one of ({}),"
742			" got {}.".format(list(self._argidx), key))
743
744			self._path = self._replace(**{key: value})
745			self._update()
746
747			def __contains__(self, item):
748			return item in self._argidx
749
750			def __repr__(self):
751			return '{}("{}")'.format(__class__.__name__, self._path)
752
753			def __str__(self):
754			return str(self._path)
755
756
757

alexsavio / hansel

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hansel.Crumb._is_crumb_arg() A

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