mandos.search.chembl.atc_search.AtcSearch.process() - Code Metrics - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

AtcSearch.process() A
last analyzed 2021-01-25 23:07 UTC

↳ Parent: mandos.search.chembl.atc_search

Complexity

Conditions

Size

Total Lines	13
Code Lines	3

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	3
nop	4
dl	0
loc	13
rs	10
c	0
b	0
f	0

from __future__ import annotations


import logging
from dataclasses import dataclass
from typing import Sequence

from pocketutils.core.dot_dict import NestedDotDict


from mandos.model import AbstractHit, ChemblCompound, Search

logger = logging.getLogger("mandos")


@dataclass(frozen=True, order=True, repr=True)
class AtcHit(AbstractHit):
    """
    An ATC code found for a compound.
    """

    level: int

    @property
    def predicate(self) -> str:
        return f"has ATC L-{self.level} code"


class AtcSearch(Search[AtcHit]):

    """"""

    def find(self, lookup: str) -> Sequence[AtcHit]:
        """

        Args:
            lookup:

        Returns:

        """
        # 'atc_classifications': ['S01HA01', 'N01BC01', 'R02AD03', 'S02DA02']
        # 'indication_class': 'Anesthetic (topical)'
        ch = self.get_compound_dot_dict(lookup)

        compound = self.compound_dot_dict_to_obj(ch)
        hits = []
        if "atc_classifications" in ch:
            for atc in ch["atc_classifications"]:
                hits.extend(self.process(lookup, compound, atc))
        return hits

    def process(self, lookup: str, compound: ChemblCompound, atc: str) -> Sequence[AtcHit]:
        """

        Args:
            lookup:
            compound:
            atc:

        Returns:

        """
        dots = NestedDotDict(self.api.atc_class.get(atc))
        return [self._code(lookup, compound, dots, 3), self._code(lookup, compound, dots, 4)]

    def _code(self, lookup: str, compound: ChemblCompound, dots: NestedDotDict, level: int):
class Foo:
    def some_method(self, x, y):
        return x + y;
        # 'level1': 'N', 'level1_description': 'NERVOUS SYSTEM', 'level2': 'N05', ...
        return AtcHit(
            None,
            compound.chid,
            compound.inchikey,
            lookup,
            compound.name,
            object_id=dots.get(f"level{level}"),
            object_name=dots.get(f"level{level}_description"),
            level=level,
        )


__all__ = ["AtcHit", "AtcSearch"]


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			import logging
4			from dataclasses import dataclass
5			from typing import Sequence
6
7			from pocketutils.core.dot_dict import NestedDotDict
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.dot_dict' Loading history...
8
9			from mandos.model import AbstractHit, ChemblCompound, Search
10
11			logger = logging.getLogger("mandos")
12
13
14			@dataclass(frozen=True, order=True, repr=True)
15			class AtcHit(AbstractHit):
16			"""
17			An ATC code found for a compound.
18			"""
19
20			level: int
21
22			@property
23			def predicate(self) -> str:
24			return f"has ATC L-{self.level} code"
25
26
27			class AtcSearch(Search[AtcHit]):
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history... introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Value 'Search' is unsubscriptable Loading history...
28			""""""
29
30			def find(self, lookup: str) -> Sequence[AtcHit]:
31			"""
32
33			Args:
34			lookup:
35
36			Returns:
37
38			"""
39			# 'atc_classifications': ['S01HA01', 'N01BC01', 'R02AD03', 'S02DA02']
40			# 'indication_class': 'Anesthetic (topical)'
41			ch = self.get_compound_dot_dict(lookup)
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "ch" 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...
42			compound = self.compound_dot_dict_to_obj(ch)
43			hits = []
44			if "atc_classifications" in ch:
45			for atc in ch["atc_classifications"]:
46			hits.extend(self.process(lookup, compound, atc))
47			return hits
48
49			def process(self, lookup: str, compound: ChemblCompound, atc: str) -> Sequence[AtcHit]:
50			"""
51
52			Args:
53			lookup:
54			compound:
55			atc:
56
57			Returns:
58
59			"""
60			dots = NestedDotDict(self.api.atc_class.get(atc))
61			return [self._code(lookup, compound, dots, 3), self._code(lookup, compound, dots, 4)]
62
63			def _code(self, lookup: str, compound: ChemblCompound, dots: NestedDotDict, level: int):
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
64			# 'level1': 'N', 'level1_description': 'NERVOUS SYSTEM', 'level2': 'N05', ...
65			return AtcHit(
66			None,
67			compound.chid,
68			compound.inchikey,
69			lookup,
70			compound.name,
71			object_id=dots.get(f"level{level}"),
72			object_name=dots.get(f"level{level}_description"),
73			level=level,
74			)
75
76
77			__all__ = ["AtcHit", "AtcSearch"]
78

dmyersturnbull / mandos

AtcSearch.process() A last analyzed 2021-01-25 23:07 UTC

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AtcSearch.process() A
last analyzed 2021-01-25 23:07 UTC