mandos.model.taxonomy._fix_tax_df() - Code Metrics - Inspection of "fix: various" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( 2b775d...83a9fb )

by Douglas
created 2021-09-23 02:56 UTC
mandos.model.taxonomy._fix_tax_df() A

↳ Parent: mandos.model.taxonomy
Complexity

Conditions
Size

Total Lines	3
Code Lines	3
Duplication

Lines	0
Ratio	0 %
Importance

Changes
Metric	Value
cc	1
eloc	3
nop	1
dl	0
loc	3
rs	10
c	0
b	0
f	0
from __future__ import annotations


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

import pandas as pd

from pocketutils.core.exceptions import LookupFailedError, DataIntegrityError


from mandos.model import MultipleMatchesError
from typeddfs import TypedDfs


from mandos.model.utils.setup import logger

from mandos.model.utils import CleverEnum


class KnownTaxa:
    """
    Taxa whose IDs are used in the code.
    """

    biota = 131567  # 2 million nodes
    eukaryota = 2759  # 1.5 million nodes
    metazoa = 33208  # 1 million
    vertebrata = 7742  # 100,000 nodes
    euteleostomi = 117571  # 100,000 nodes
    human = 9606
    rat = 10116
    mouse = 10090


class NameType(CleverEnum):
    """
    Scientific name, common name, or mnemonic.
    """

    scientific = enum.auto()
    common = enum.auto()
    mnemonic = enum.auto()


TaxonomyDf = (
    TypedDfs.typed("TaxonomyDf")
    .require("taxon", "parent", dtype=int)
    .require("mnemonic", "scientific_name", "common_name", dtype=str)
    .strict()
    .secure()
).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
    __scientific_name: str
    __common_name: Optional[str]
    __mnemonic: Optional[str]
    __parent: Optional[Taxon]
    __children: Set[Taxon]

    @property
    def id(self) -> int:

        """
        Returns the UniProt ID of this taxon.
        """
        return self.__id

    @property
    def scientific_name(self) -> str:
        """
        Returns the scientific name of this taxon.
        """
        return self.__scientific_name

    @property
    def common_name(self) -> Optional[str]:
        """
        Returns the common name of this taxon, or None if it has none.
        """
        return self.__common_name

    @property
    def mnemonic(self) -> Optional[str]:
        """
        Returns the mnemonic of this taxon, or None if it has none.
        Only ~16 taxa have mnemonics as of 2021-08.
        For example: "BOVIN" `<https://www.uniprot.org/taxonomy/9913>`_.
        """
        return self.__mnemonic

    @property
    def keys(self) -> FrozenSet[Union[int, str]]:
        """
        Returns the IDs and names that can be used to find this taxon.
        Specifically, includes the ID (int), scientific name (str),
        common name (str; if any), and mnemonic (str; if any).
        """
        keys = {self.id, self.scientific_name, self.common_name, self.mnemonic}
        return frozenset({s for s in keys if s is not None})

    @property
    def as_series(self) -> pd.Series:

        return pd.Series(
            dict(
                taxon=self.id,
                scientific_name=self.scientific_name,
                common_name=self.common_name,
                mnemonic=self.mnemonic,
                parent=self.parent.id,
            )
        )

    @property
    def parent(self) -> Taxon:
        """
        Returns the parent of this taxon.
        """
        return self.__parent

    @property
    def children(self) -> Set[Taxon]:
        """
        Returns the immediate descendents of this taxon.
        """
        return set(self.__children)

    @property
    def ancestors(self) -> Sequence[Taxon]:
        """
        Returns all taxa that are ancestors of, or identical to, this taxon.
        """
        lst = []
        self._ancestors(lst)
        return lst

    @property
    def descendents(self) -> Sequence[Taxon]:
        """
        Returns all taxa that are descendents of, or identical to, this taxon.
        """
        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):
        parent = self.parent.id if self.parent else "none"
        return f"{self.__class__.__name__}({self.id}: {self.scientific_name} (parent={parent}))"

    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


TaxaIdsAndNames = Union[int, str, Taxon, Iterable[Union[int, str, Taxon]]]
TaxonIdOrName = Union[int, str, Taxon]


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

    def set_names(self, scientific: str, common: Optional[str], mnemonic: Optional[str]):

        self.__scientific_name = scientific
        self.__common_name = common
        self.__mnemonic = mnemonic

    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.scientific_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_trees(cls, taxonomies: Sequence[Taxonomy]) -> Taxonomy:

        # we need to rewrite the ancestors, which from_df already does
        # so we'll just use that
        dfs = [tree.to_df() for tree in taxonomies]
        df = TaxonomyDf(pd.concat(dfs, ignore_index=True))

        df = df.drop_duplicates().sort_values("taxon")

        return Taxonomy.from_df(df)

    @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
        if 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
            raise DataIntegrityError(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:
        """
        Reads from a DataFrame file.
        """
        df = TaxonomyDf.read_file(path)

        return cls.from_df(df)

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

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

        Args:
            df: A TaxonomyDf DataFrame

        Returns:
            The corresponding taxonomic tree
        """
        # just build up a tree, sticking the elements in by_id
        tax = {}
        for row in df.itertuples():
            _new_child = _Taxon(
                row.taxon, row.scientific_name, row.common_name, row.mnemonic, None, set()
            )
            child = tax.setdefault(row.taxon, _new_child)
            child.set_names(row.scientific_name, row.common_name, row.mnemonic)
            if row.parent != 0:
                _new_parent = _Taxon(row.parent, "", None, None, None, set())
                parent = tax.setdefault(row.parent, _new_parent)
                child.set_parent(parent)
                parent.add_child(child)
        bad = [t for t in tax.values() if t.scientific_name.strip() == ""]
        if len(bad) > 0:
            raise DataIntegrityError(
                f"{len(bad)} taxa with missing or empty scientific 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.convert(pd.DataFrame([taxon.as_series for taxon in self.taxa]))

    @property
    def taxa(self) -> Sequence[Taxon]:
        """
        Returns all taxa in the tree.
        """
        return list(self._by_id.values())

    @property
    def roots(self) -> Sequence[Taxon]:
        """
        Returns the roots of the tree (at least 1).
        """
        return [k for k in self.taxa if k.parent is None or k.parent not in self]

    @property
    def leaves(self) -> Sequence[Taxon]:
        """
        Returns the leaves (typically species or sub-species) of the tree.
        """
        return [k for k in self.taxa if len(k.children) == 0]

    def exclude_subtree(self, item: Union[int, Taxon]) -> Taxonomy:
        """
        Returns a new tree that excludes a single specified taxon and its descendents.
        """
        descendents = self.get_by_id_or_name(item)
        for i in set(descendents):
            descendents += i.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 exclude_subtrees_by_ids_or_names(self, items: TaxaIdsAndNames) -> Taxonomy:
        """
        Returns a tree tree that excludes taxa that are descendents of the specified taxa.
        If a name is used in multiple taxa, all of those will be used to exclude.

        Arguments:
            items: A scientific name, common name, or mnemonic; or a sequence of them
        """
        if isinstance(items, (int, str, Taxon)):
            items = [items]
        bad_taxa = self.subtrees_by_ids_or_names(items).taxa
        by_id = {i: t for i, t in self._by_id.items() if i not in bad_taxa}
        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 subtree(self, item: int) -> Taxonomy:
        """
        Returns the tree that is rooted at a single taxon (by ID).
        """
        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_ids_or_names(self, items: TaxaIdsAndNames) -> Taxonomy:
        """
        Returns the tree that is rooted at the specified taxa (by name or ID).
        The tree will have *at most* ``len(items)`` roots.

        Arguments:
            items: A scientific name, common name, or mnemonic; or a sequence of them
        """
        if isinstance(items, (int, str, Taxon)):
            items = [items]
        descendents: Set[Taxon] = set()
        for item in items:
            for taxon in self.get_by_id_or_name(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 subtrees_by_name(self, item: str) -> Taxonomy:
        """
        Returns the tree rooted at the taxa with the specified scientific name.

        Arguments:
            item: A scientific name, common name, or mnemonic
        """
        return self.subtrees_by_names(item)

    def subtrees_by_names(self, items: Iterable[str]) -> Taxonomy:
        """
        Returns the tree rooted at the specified taxa (by scientific name).

        Arguments:
            items: A sequence of scientific name, common name, and/or mnemonics
        """
        descendents: Set[Taxon] = set()
        for item in items:
            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.

        Arguments:
            item: A scientific name, common name, or mnemonic

        Raises:
            LookupError: If not found
            MultipleMatchesError: If multiple are found
        """
        one = self.get_one_by_name(item)
        if one is None:
            raise LookupFailedError(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.

        Arguments:
            item: A scientific name, common name, or mnemonic

        Raises:
            LookupError: If not found
            MultipleMatchesError: If multiple are found
        """
        taxa = self.get_by_name(item)
        ids = ",".join([str(t.id) for t in taxa])
        if len(taxa) > 1:

            raise MultipleMatchesError(f"Got multiple results for {item}: {ids}")
        elif len(taxa) == 0:
            raise LookupFailedError(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``.
        Logs at warning level if multiple matched.

        Arguments:
            item: A scientific name, common name, or mnemonic
        """
        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.scientific_name
        return self._by_name.get(item, frozenset(set()))

    def get_all_by_id_or_name(self, items: Iterable[Union[int, str, Taxon]]) -> FrozenSet[Taxon]:
        """
        Gets all taxa that match any number of IDs or names.
        """
        matching = []
        for item in items:
            matching += self.get_by_id_or_name(item)
        # finally de-duplicates (making this fn useful)
        return frozenset(matching)

    def get_by_id_or_name(self, item: Union[int, str, Taxon]) -> FrozenSet[Taxon]:
        """
        Gets all taxa that match an ID or name.
        """
        if isinstance(item, Taxon):
            item = item.id
        if isinstance(item, int):

            taxon = self._by_id.get(item)
            return frozenset([]) if taxon is None else frozenset([taxon])
        elif isinstance(item, str):
            return self._by_name.get(item, frozenset(set()))
        else:
            raise XTypeError(f"Unknown type {type(item)} of {item}")


    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: Union[int, Taxon]) -> 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 XTypeError(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 LookupFailedError(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.scientific_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)
        # put these in the right order
        # so that we favor mnemonic, then scientific name, then common name
        for t in tax:

            if t.mnemonic is not None:
                by_name[t.mnemonic].add(t)
        for t in tax:

            by_name[t.scientific_name].add(t)
        for t in tax:

            if t.common_name is not None:
                by_name[t.common_name].add(t)
        # NOTE: lower-casing the keys for lookup
        return {k.lower(): frozenset(v) for k, v in by_name.items()}


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

dmyersturnbull / mandos

Push — main ( 2b775d...83a9fb )

mandos.model.taxonomy._fix_tax_df() A

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