mandos.model.taxonomy - Code Metrics - Inspection of "feat: tests and taxa by name" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — main ( 4e4203...cdf0f7 )

by Douglas

created 2021-04-01 01:10 UTC

mandos.model.taxonomy F

↳ Parent: Project

Complexity

Total Complexity

Size/Duplication

Total Lines	378
Duplicated Lines	0 %

Importance

Changes

Metric	Value
eloc	201
dl	0
loc	378
rs	3.36
c	0
b	0
f	0
wmc	63

45 Methods

Rating	Name	Size	Complexity
A	_Taxon.__str__()	2	1
A	Taxon._ancestors()	3	1
A	Taxon.children()	8	1
A	Taxon.__lt__()	2	1
A	Taxon.__str__()	2	1
A	Taxon.__repr__()	2	1
A	Taxon.__eq__()	2	1
A	Taxon.__hash__()	2	1
A	_Taxon.__lt__()	2	1
A	Taxon._descendents()	4	2
A	_Taxon.__eq__()	2	1
A	_Taxon.__repr__()	2	1
A	Taxon.descendents()	10	1
A	Taxon.ancestors()	10	1
A	_Taxon.__hash__()	2	1
A	Taxon.id()	8	1
A	_Taxon.add_child()	2	1
A	_Taxon.set_parent()	2	1
A	Taxon.parent()	8	1
A	_Taxon.set_name()	2	1
A	Taxon.name()	8	1
A	Taxonomy.__len__()	2	1
A	Taxonomy.n_taxa()	2	1
A	Taxonomy.subtree()	6	1
A	Taxonomy.__getitem__()	17	2
A	Taxonomy.roots()	8	1
A	Taxonomy.from_list()	8	1
A	Taxonomy.get_by_name()	7	2
A	Taxonomy.req_only_by_name()	12	3
A	Taxonomy.to_df()	5	1
A	Taxonomy.subtrees_by_name()	10	2
A	Taxonomy.from_path()	4	1
A	Taxonomy.contains()	2	1
A	Taxonomy.taxa()	8	1
A	Taxonomy.__contains__()	2	1
A	Taxonomy.req_one_by_name()	10	2
A	Taxonomy.req()	8	2
B	Taxonomy.from_df()	31	5
A	Taxonomy.leaves()	3	1
A	Taxonomy.get_one_by_name()	13	3
A	Taxonomy._build_by_name()	6	2
A	Taxonomy.get()	16	3
A	Taxonomy.__init__()	12	2
A	Taxonomy.__str__()	2	1
A	Taxonomy.__repr__()	3	1

How to fix Complexity

from __future__ import annotations


from collections import defaultdict
from dataclasses import dataclass
from functools import total_ordering
from pathlib import Path
from typing import List, Mapping, Optional, Sequence, Set, Union, FrozenSet, Iterable

import pandas as pd

from typeddfs import TypedDfs


from mandos import logger

TaxonomyDf = (
    TypedDfs.typed("TaxonomyDf").require("taxon").require("parent").require("scientific_name")
).build()


@total_ordering

@dataclass()
class Taxon:
    """"""

    # we can't use frozen=True because we have both parents and children
    # instead, just use properties
    __id: int
    __name: str
    __parent: Optional[Taxon]
    __children: Set[Taxon]

    @property
    def id(self) -> int:

        """

        Returns:

        """
        return self.__id

    @property
    def name(self) -> str:
        """

        Returns:

        """
        return self.__name

    @property
    def parent(self) -> Taxon:
        """

        Returns:

        """
        return self.__parent

    @property
    def children(self) -> Set[Taxon]:
        """

        Returns:

        """
        return set(self.__children)

    @property
    def ancestors(self) -> Sequence[Taxon]:
        """

        Returns:

        """
        lst = []
        self._ancestors(lst)
        return lst

    @property
    def descendents(self) -> Sequence[Taxon]:
        """

        Returns:

        """
        lst = []
        self._descendents(lst)
        return lst

    def _ancestors(self, values: List[Taxon]) -> None:
        values.append(self.parent)
        self.parent._ancestors(values)
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

    def _descendents(self, values: List[Taxon]) -> None:
        values.extend(self.children)
        for child in self.children:
            child._descendents(values)
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

    def __str__(self):
        return repr(self)

    def __repr__(self):
        return f"{self.__class__.__name__}({self.id}: {self.name} (parent={self.parent.id if self.parent else 'none'}))"


    def __hash__(self):
        return hash(self.id)

    def __eq__(self, other):
        return self.id == other.id

    def __lt__(self, other):
        return self.id < other.id


@dataclass()
class _Taxon(Taxon):
    """
    An internal, modifiable taxon for building the tree.
    """

    def set_name(self, name: str):

        self.__name = name

    def set_parent(self, parent: _Taxon):

        self.__parent = parent

    def add_child(self, child: _Taxon):

        self.__children.add(child)

    # weirdly these are required again -- probably an issue with dataclass

    def __str__(self):
        return repr(self)

    def __repr__(self):
        return f"{self.__class__.__name__}({self.id}: {self.name} (parent={self.parent.id if self.parent else 'none'}))"


    def __hash__(self):
        return hash(self.id)

    def __eq__(self, other):
        return self.id == other.id

    def __lt__(self, other):
        return self.id < other.id


class Taxonomy:
    """
    A taxonomic tree of organisms from UniProt.
    Elements in the tree can be looked up by name or ID using ``__getitem__`` and ``get``.
    """

    def __init__(self, by_id: Mapping[int, Taxon], by_name: Mapping[str, FrozenSet[Taxon]]):
        """

        Args:
            by_id:
        """
        # constructor provided for consistency with the members
        self._by_id = dict(by_id)
        self._by_name = dict(by_name)
        # this probably isn't actually possible
        if len(self) == 0:
            logger.warning(f"{self} contains 0 taxa")

    @classmethod
    def from_list(cls, taxa: Sequence[Taxon]) -> Taxonomy:

        by_id = {x.id: x for x in taxa}
        by_name = cls._build_by_name(by_id.values())
        tax = Taxonomy(by_id, by_name)
        # catch duplicate values
        assert len(tax._by_id) == len(taxa), f"{len(tax._by_id)} != {len(taxa)}"
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
        return tax

    @classmethod
    def from_path(cls, path: Path) -> Taxonomy:

        df = pd.read_csv(path, sep="\t", header=0)

        return cls.from_df(df)

    @classmethod
    def from_df(cls, df: TaxonomyDf) -> Taxonomy:

        """
        Reads from a DataFrame from a CSV file provided by a UniProt download.
        Strips any entries with missing or empty-string scientific names.

        Args:
            df: A dataframe with columns (at least) "taxon", "scientific_name", and "parent"

        Returns:
            The corresponding taxonomic tree
        """
        df["taxon"] = df["taxon"].astype(int)
        # TODO fillna(0) should not be needed

        df["parent"] = df["parent"].fillna(0).astype(int)
        # just build up a tree, sticking the elements in by_id
        tax = {}
        for row in df.itertuples():
            child = tax.setdefault(row.taxon, _Taxon(row.taxon, row.scientific_name, None, set()))
            child.set_name(row.scientific_name)
            if row.parent != 0:
                parent = tax.setdefault(row.parent, _Taxon(row.parent, "", None, set()))
                child.set_parent(parent)
                parent.add_child(child)
        bad = [t for t in tax.values() if t.name.strip() == ""]
        if len(bad) > 0:
            raise ValueError(f"There are taxa with missing or empty names: {bad}.")
        for v in tax.values():

            v.__class__ = Taxon
        by_name = cls._build_by_name(tax.values())
        return Taxonomy(tax, by_name)

    def to_df(self) -> TaxonomyDf:

        return TaxonomyDf(
            [
                pd.Series(dict(taxon=taxon.id, scientific_name=taxon.name, parent=taxon.parent.id))
                for taxon in self.taxa
            ]
        )

    @property
    def taxa(self) -> Sequence[Taxon]:
        """

        Returns:

        """
        return list(self._by_id.values())

    @property
    def roots(self) -> Sequence[Taxon]:
        """

        Returns:

        """
        return [k for k in self.taxa if k.parent is None or k.parent not in self]

    @property
    def leaves(self) -> Sequence[Taxon]:

        return [k for k in self.taxa if len(k.children) == 0]

    def subtree(self, item: int) -> Taxonomy:

        item = self[item]
        descendents = {item, *item.descendents}
        by_id = {d.id: d for d in descendents}
        by_name = self.__class__._build_by_name(by_id.values())
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
        return Taxonomy(by_id, by_name)

    def subtrees_by_name(self, item: str) -> Taxonomy:
        """
        Returns the taxonomy that rooted at each of the taxa with the specified scientific name.
        """
        descendents: Set[Taxon] = set()
        for taxon in self._by_name.get(item, []):
            descendents.update({taxon, *taxon.descendents})
        by_id = {d.id: d for d in descendents}
        by_name = self.__class__._build_by_name(by_id.values())
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
        return Taxonomy(by_id, by_name)

    def req_one_by_name(self, item: str) -> Taxon:
        """
        Gets a single taxon by its name.
        If there are multiple, returns the first (lowest ID).
        Raises an error if there are no matches.
        """
        one = self.get_one_by_name(item)
        if one is None:
            raise LookupError(f"No taxa for {item}")
        return one

    def req_only_by_name(self, item: str) -> Taxon:
        """
        Gets a single taxon by its name.
        Raises an error if there are multiple matches for the name, or if there are no matches.
        """
        taxa = self.get_by_name(item)
        ids = ",".join([str(t.id) for t in taxa])
        if len(taxa) > 1:

            raise ValueError(f"Got multiple results for {item}: {ids}")
        elif len(taxa) == 0:
            raise LookupError(f"No taxa for {item}")
        return next(iter(taxa))

    def get_one_by_name(self, item: str) -> Optional[Taxon]:
        """
        Gets a single taxon by its name.
        If there are multiple, returns the first (lowest ID).
        If there are none, returns ``None``.
        """
        taxa = self.get_by_name(item)
        ids = ",".join([str(t.id) for t in taxa])
        if len(taxa) > 1:
            logger.warning(f"Got multiple results for {item}: {ids}")
        elif len(taxa) == 0:
            return None
        return next(iter(taxa))

    def get_by_name(self, item: str) -> FrozenSet[Taxon]:
        """
        Gets all taxa that match a scientific name.
        """
        if isinstance(item, Taxon):
            item = item.name
        return self._by_name.get(item, frozenset(set()))

    def req(self, item: int) -> Taxon:
        """
        Gets a single taxon by its ID.
        Raises an error if it is not found.
        """
        if isinstance(item, Taxon):
            item = item.id
        return self[item]

    def get(self, item: int) -> Optional[Taxon]:
        """
        Corresponds to ``dict.get``.

        Args:
            item: The scientific name or UniProt ID

        Returns:
            The taxon, or None if it was not found
        """
        if isinstance(item, Taxon):
            item = item.id
        if isinstance(item, int):

            return self._by_id.get(item)
        else:
            raise TypeError(f"Type {type(item)} of {item} not applicable")

    def __getitem__(self, item: int) -> Taxon:
        """
        Corresponds to ``dict[_]``.

        Args:
            item: The UniProt ID

        Returns:
            The taxon

        Raises:
            KeyError: If the taxon was not found
        """
        got = self.get(item)
        if got is None:
            raise KeyError(f"{item} not found in {self}")
        return got

    def contains(self, item: Union[Taxon, int, str]):

        return self.get(item) is not None

    def n_taxa(self) -> int:

        return len(self._by_id)

    def __contains__(self, item: Union[Taxon, int, str]):
        return self.get(item) is not None

    def __len__(self) -> int:
        return len(self._by_id)

    def __str__(self) -> str:
        return repr(self)

    def __repr__(self) -> str:
        roots = ", ".join(r.name for r in self.roots)
        return f"{self.__class__.__name__}(n={len(self._by_id)} (roots={roots}) @ {hex(id(self))})"

    @classmethod
    def _build_by_name(cls, tax: Iterable[Taxon]) -> Mapping[str, FrozenSet[Taxon]]:
        by_name = defaultdict(set)
        for t in tax:

            by_name[t.name].add(t)
        return {k: frozenset(v) for k, v in by_name.items()}


__all__ = ["Taxon", "Taxonomy", "TaxonomyDf"]


1			from __future__ import annotations
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2
3			from collections import defaultdict
4			from dataclasses import dataclass
5			from functools import total_ordering
6			from pathlib import Path
7			from typing import List, Mapping, Optional, Sequence, Set, Union, FrozenSet, Iterable
8
9			import pandas as pd
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'pandas' Loading history...
10			from typeddfs import TypedDfs
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'typeddfs' Loading history...
11
12			from mandos import logger
13
14			TaxonomyDf = (
15			TypedDfs.typed("TaxonomyDf").require("taxon").require("parent").require("scientific_name")
16			).build()
17
18
19			@total_ordering
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
20			@dataclass()
21			class Taxon:
22			""""""
23
24			# we can't use frozen=True because we have both parents and children
25			# instead, just use properties
26			__id: int
27			__name: str
28			__parent: Optional[Taxon]
29			__children: Set[Taxon]
30
31			@property
32			def id(self) -> int:
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Attribute name "id" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
33			"""
34
35			Returns:
36
37			"""
38			return self.__id
39
40			@property
41			def name(self) -> str:
42			"""
43
44			Returns:
45
46			"""
47			return self.__name
48
49			@property
50			def parent(self) -> Taxon:
51			"""
52
53			Returns:
54
55			"""
56			return self.__parent
57
58			@property
59			def children(self) -> Set[Taxon]:
60			"""
61
62			Returns:
63
64			"""
65			return set(self.__children)
66
67			@property
68			def ancestors(self) -> Sequence[Taxon]:
69			"""
70
71			Returns:
72
73			"""
74			lst = []
75			self._ancestors(lst)
76			return lst
77
78			@property
79			def descendents(self) -> Sequence[Taxon]:
80			"""
81
82			Returns:
83
84			"""
85			lst = []
86			self._descendents(lst)
87			return lst
88
89			def _ancestors(self, values: List[Taxon]) -> None:
90			values.append(self.parent)
91			self.parent._ancestors(values)
			0 ignored issues – show Coding Style Best Practice introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report It seems like `_ancestors` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
92
93			def _descendents(self, values: List[Taxon]) -> None:
94			values.extend(self.children)
95			for child in self.children:
96			child._descendents(values)
			0 ignored issues – show Coding Style Best Practice introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report It seems like `_descendents` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
97
98			def __str__(self):
99			return repr(self)
100
101			def __repr__(self):
102			return f"{self.__class__.__name__}({self.id}: {self.name} (parent={self.parent.id if self.parent else 'none'}))"
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (120/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
103
104			def __hash__(self):
105			return hash(self.id)
106
107			def __eq__(self, other):
108			return self.id == other.id
109
110			def __lt__(self, other):
111			return self.id < other.id
112
113
114			@dataclass()
115			class _Taxon(Taxon):
116			"""
117			An internal, modifiable taxon for building the tree.
118			"""
119
120			def set_name(self, name: str):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
121			self.__name = name
122
123			def set_parent(self, parent: _Taxon):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
124			self.__parent = parent
125
126			def add_child(self, child: _Taxon):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
127			self.__children.add(child)
128
129			# weirdly these are required again -- probably an issue with dataclass
130
131			def __str__(self):
132			return repr(self)
133
134			def __repr__(self):
135			return f"{self.__class__.__name__}({self.id}: {self.name} (parent={self.parent.id if self.parent else 'none'}))"
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (120/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
136
137			def __hash__(self):
138			return hash(self.id)
139
140			def __eq__(self, other):
141			return self.id == other.id
142
143			def __lt__(self, other):
144			return self.id < other.id
145
146
147			class Taxonomy:
148			"""
149			A taxonomic tree of organisms from UniProt.
150			Elements in the tree can be looked up by name or ID using ``__getitem__`` and ``get``.
151			"""
152
153			def __init__(self, by_id: Mapping[int, Taxon], by_name: Mapping[str, FrozenSet[Taxon]]):
154			"""
155
156			Args:
157			by_id:
158			"""
159			# constructor provided for consistency with the members
160			self._by_id = dict(by_id)
161			self._by_name = dict(by_name)
162			# this probably isn't actually possible
163			if len(self) == 0:
164			logger.warning(f"{self} contains 0 taxa")
165
166			@classmethod
167			def from_list(cls, taxa: Sequence[Taxon]) -> Taxonomy:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
168			by_id = {x.id: x for x in taxa}
169			by_name = cls._build_by_name(by_id.values())
170			tax = Taxonomy(by_id, by_name)
171			# catch duplicate values
172			assert len(tax._by_id) == len(taxa), f"{len(tax._by_id)} != {len(taxa)}"
			0 ignored issues – show Coding Style Best Practice introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report It seems like `_by_id` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
173			return tax
174
175			@classmethod
176			def from_path(cls, path: Path) -> Taxonomy:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
177			df = pd.read_csv(path, sep="\t", header=0)
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
178			return cls.from_df(df)
179
180			@classmethod
181			def from_df(cls, df: TaxonomyDf) -> Taxonomy:
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Argument name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
182			"""
183			Reads from a DataFrame from a CSV file provided by a UniProt download.
184			Strips any entries with missing or empty-string scientific names.
185
186			Args:
187			df: A dataframe with columns (at least) "taxon", "scientific_name", and "parent"
188
189			Returns:
190			The corresponding taxonomic tree
191			"""
192			df["taxon"] = df["taxon"].astype(int)
193			# TODO fillna(0) should not be needed
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report `TODO` and `FIXME` comments should generally be avoided. Loading history...
194			df["parent"] = df["parent"].fillna(0).astype(int)
195			# just build up a tree, sticking the elements in by_id
196			tax = {}
197			for row in df.itertuples():
198			child = tax.setdefault(row.taxon, _Taxon(row.taxon, row.scientific_name, None, set()))
199			child.set_name(row.scientific_name)
200			if row.parent != 0:
201			parent = tax.setdefault(row.parent, _Taxon(row.parent, "", None, set()))
202			child.set_parent(parent)
203			parent.add_child(child)
204			bad = [t for t in tax.values() if t.name.strip() == ""]
205			if len(bad) > 0:
206			raise ValueError(f"There are taxa with missing or empty names: {bad}.")
207			for v in tax.values():
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "v" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
208			v.__class__ = Taxon
209			by_name = cls._build_by_name(tax.values())
210			return Taxonomy(tax, by_name)
211
212			def to_df(self) -> TaxonomyDf:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
213			return TaxonomyDf(
214			[
215			pd.Series(dict(taxon=taxon.id, scientific_name=taxon.name, parent=taxon.parent.id))
216			for taxon in self.taxa
217			]
218			)
219
220			@property
221			def taxa(self) -> Sequence[Taxon]:
222			"""
223
224			Returns:
225
226			"""
227			return list(self._by_id.values())
228
229			@property
230			def roots(self) -> Sequence[Taxon]:
231			"""
232
233			Returns:
234
235			"""
236			return [k for k in self.taxa if k.parent is None or k.parent not in self]
237
238			@property
239			def leaves(self) -> Sequence[Taxon]:
			0 ignored issues – show introduced 2021-03-16 18:40 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
240			return [k for k in self.taxa if len(k.children) == 0]
241
242			def subtree(self, item: int) -> Taxonomy:
			0 ignored issues – show introduced 2021-03-16 18:40 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
243			item = self[item]
244			descendents = {item, *item.descendents}
245			by_id = {d.id: d for d in descendents}
246			by_name = self.__class__._build_by_name(by_id.values())
			0 ignored issues – show Coding Style Best Practice introduced 2021-04-01 01:11 UTC by Report Bug Copy Issue Report It seems like `_build_by_name` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
247			return Taxonomy(by_id, by_name)
248
249			def subtrees_by_name(self, item: str) -> Taxonomy:
250			"""
251			Returns the taxonomy that rooted at each of the taxa with the specified scientific name.
252			"""
253			descendents: Set[Taxon] = set()
254			for taxon in self._by_name.get(item, []):
255			descendents.update({taxon, *taxon.descendents})
256			by_id = {d.id: d for d in descendents}
257			by_name = self.__class__._build_by_name(by_id.values())
			0 ignored issues – show Coding Style Best Practice introduced 2021-04-01 01:11 UTC by Report Bug Copy Issue Report It seems like `_build_by_name` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
258			return Taxonomy(by_id, by_name)
259
260			def req_one_by_name(self, item: str) -> Taxon:
261			"""
262			Gets a single taxon by its name.
263			If there are multiple, returns the first (lowest ID).
264			Raises an error if there are no matches.
265			"""
266			one = self.get_one_by_name(item)
267			if one is None:
268			raise LookupError(f"No taxa for {item}")
269			return one
270
271			def req_only_by_name(self, item: str) -> Taxon:
272			"""
273			Gets a single taxon by its name.
274			Raises an error if there are multiple matches for the name, or if there are no matches.
275			"""
276			taxa = self.get_by_name(item)
277			ids = ",".join([str(t.id) for t in taxa])
278			if len(taxa) > 1:
			0 ignored issues – show Unused Code introduced 2021-04-01 01:11 UTC by Report Bug Copy Issue Report Unnecessary "elif" after "raise" Loading history...
279			raise ValueError(f"Got multiple results for {item}: {ids}")
280			elif len(taxa) == 0:
281			raise LookupError(f"No taxa for {item}")
282			return next(iter(taxa))
283
284			def get_one_by_name(self, item: str) -> Optional[Taxon]:
285			"""
286			Gets a single taxon by its name.
287			If there are multiple, returns the first (lowest ID).
288			If there are none, returns ``None``.
289			"""
290			taxa = self.get_by_name(item)
291			ids = ",".join([str(t.id) for t in taxa])
292			if len(taxa) > 1:
293			logger.warning(f"Got multiple results for {item}: {ids}")
294			elif len(taxa) == 0:
295			return None
296			return next(iter(taxa))
297
298			def get_by_name(self, item: str) -> FrozenSet[Taxon]:
299			"""
300			Gets all taxa that match a scientific name.
301			"""
302			if isinstance(item, Taxon):
303			item = item.name
304			return self._by_name.get(item, frozenset(set()))
305
306			def req(self, item: int) -> Taxon:
307			"""
308			Gets a single taxon by its ID.
309			Raises an error if it is not found.
310			"""
311			if isinstance(item, Taxon):
312			item = item.id
313			return self[item]
314
315			def get(self, item: int) -> Optional[Taxon]:
316			"""
317			Corresponds to ``dict.get``.
318
319			Args:
320			item: The scientific name or UniProt ID
321
322			Returns:
323			The taxon, or None if it was not found
324			"""
325			if isinstance(item, Taxon):
326			item = item.id
327			if isinstance(item, int):
			0 ignored issues – show unused-code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history...
328			return self._by_id.get(item)
329			else:
330			raise TypeError(f"Type {type(item)} of {item} not applicable")
331
332			def __getitem__(self, item: int) -> Taxon:
333			"""
334			Corresponds to ``dict[_]``.
335
336			Args:
337			item: The UniProt ID
338
339			Returns:
340			The taxon
341
342			Raises:
343			KeyError: If the taxon was not found
344			"""
345			got = self.get(item)
346			if got is None:
347			raise KeyError(f"{item} not found in {self}")
348			return got
349
350			def contains(self, item: Union[Taxon, int, str]):
			0 ignored issues – show introduced 2021-04-01 01:11 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
351			return self.get(item) is not None
352
353			def n_taxa(self) -> int:
			0 ignored issues – show introduced 2021-04-01 01:11 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
354			return len(self._by_id)
355
356			def __contains__(self, item: Union[Taxon, int, str]):
357			return self.get(item) is not None
358
359			def __len__(self) -> int:
360			return len(self._by_id)
361
362			def __str__(self) -> str:
363			return repr(self)
364
365			def __repr__(self) -> str:
366			roots = ", ".join(r.name for r in self.roots)
367			return f"{self.__class__.__name__}(n={len(self._by_id)} (roots={roots}) @ {hex(id(self))})"
368
369			@classmethod
370			def _build_by_name(cls, tax: Iterable[Taxon]) -> Mapping[str, FrozenSet[Taxon]]:
371			by_name = defaultdict(set)
372			for t in tax:
			0 ignored issues – show Coding Style Naming introduced 2021-04-01 01:11 UTC by Report Bug Copy Issue Report Variable name "t" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
373			by_name[t.name].add(t)
374			return {k: frozenset(v) for k, v in by_name.items()}
375
376
377			__all__ = ["Taxon", "Taxonomy", "TaxonomyDf"]
378

dmyersturnbull / mandos

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