mandos.model.chembl_support.chembl_targets.TargetFactory.__init__() - Code Metrics - Inspection of "feat: improve strategies and traversal" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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by Douglas

created 2021-03-13 01:10 UTC

TargetFactory.init() A

↳ Parent: mandos.model.chembl_support.chembl_targets

Complexity

Conditions

Size

Total Lines	2
Code Lines	2

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	2
nop	2
dl	0
loc	2
rs	10
c	0
b	0
f	0

"""
Model of ChEMBL targets and a hierarchy between them as a directed acyclic graph (DAG).
"""
from __future__ import annotations

import enum
import logging
from dataclasses import dataclass
from typing import Optional, Set

from urllib3.util.retry import MaxRetryError

from pocketutils.core.dot_dict import NestedDotDict


from mandos.model.chembl_api import ChemblApi

logger = logging.getLogger(__package__)


class TargetNotFoundError(ValueError):

    """"""


class TargetType(enum.Enum):
    """
    Enum corresponding to the ChEMBL API field ``target.target_type``.
    """

    single_protein = enum.auto()
    protein_family = enum.auto()
    protein_complex = enum.auto()
    protein_complex_group = enum.auto()
    selectivity_group = enum.auto()
    protein_protein_interaction = enum.auto()
    nucleic_acid = enum.auto()
    chimeric_protein = enum.auto()
    protein_nucleic_acid_complex = enum.auto()
    metal = enum.auto()
    small_molecule = enum.auto()
    subcellular = enum.auto()
    unknown = enum.auto()

    @classmethod
    def of(cls, s: str) -> TargetType:

        key = s.replace(" ", "_").replace("-", "_").lower()
        try:
            return TargetType[key]
        except KeyError:
            logger.error(f"Target type {key} not found. Using TargetType.unknown.")

            return TargetType.unknown

    @classmethod
    def protein_types(cls) -> Set[TargetType]:
        """
        Returns the target types that are expressly proteins.
        Specifically, single proteins, protein complexes, protein complex groups, and protein families.

        This does **not** include protein-protein interactions, chimeric proteins,
        protein-nucleic acid complexes, or selectivity groups.
        """
        return {s for s in cls if s.is_protein}

    @classmethod
    def all_types(cls) -> Set[TargetType]:

        return set(TargetType)  # here for symmetry

    @property
    def is_traversable(self) -> bool:
        """
        Returns the target types that can have relationships defined on them.
        Note that this may not match ChEMBL's own definition --
        there may be types (e.g. protein_protein_interaction) that have relationships.
        Those rare types are not included here.
        """
        return self in {
            TargetType.single_protein,
            TargetType.protein_family,
            TargetType.protein_complex,
            TargetType.protein_complex_group,
            TargetType.selectivity_group,
        }

    @property
    def is_protein(self) -> bool:
        """
        Whether this type is a "protein".
        Specifically, single proteins, protein complexes, protein complex groups, and protein families.

        This does **not** include protein-protein interactions, chimeric proteins,
        protein-nucleic acid complexes, or selectivity groups.
        """
        return self in {
            TargetType.single_protein,
            TargetType.protein_family,
            TargetType.protein_complex,
            TargetType.protein_complex_group,
        }

    @property
    def is_unknown(self) -> bool:
        """
        Returns whether this is the "unkown" type.
        In principle, this could have a more involved meaning.
        """
        return self == TargetType.unknown


@dataclass(frozen=True, order=True, repr=True)
class ChemblTarget:
    """
    A target from ChEMBL, from the ``target`` table.

    Attributes:
        chembl: The CHEMBL ID, starting with 'CHEMBL'
        name: The preferred name (``pref_target_name``)
        type: From the ``target_type`` ChEMBL field
    """

    chembl: str
    name: Optional[str]
    type: TargetType


class TargetFactory:
    """
    Factory for ``Target`` that injects a ``ChemblApi``.
    """

    def __init__(self, api: ChemblApi):
        self.api = api

    def find(self, chembl: str) -> ChemblTarget:
        """

        Args:
            chembl:

        Returns:
            A ``Target`` instance from a newly created subclass of that class
        """

        try:
            targets = self.api.target.filter(target_chembl_id=chembl)
        except MaxRetryError:
            raise TargetNotFoundError(f"Failed to find target {chembl}")
        assert len(targets) == 1, f"Found {len(targets)} targets for {chembl}"
        target = NestedDotDict(targets[0])
        return ChemblTarget(
            chembl=target["target_chembl_id"],
            name=target.get("pref_name"),
            type=TargetType.of(target["target_type"]),
        )


__all__ = [
    "TargetType",
    "TargetFactory",
    "TargetNotFoundError",
    "ChemblTarget",
]


1			"""
2			Model of ChEMBL targets and a hierarchy between them as a directed acyclic graph (DAG).
3			"""
4			from __future__ import annotations
5
6			import enum
7			import logging
8			from dataclasses import dataclass
9			from typing import Optional, Set
10
11			from urllib3.util.retry import MaxRetryError
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'urllib3.util.retry' Loading history...
12			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...
13
14			from mandos.model.chembl_api import ChemblApi
15
16			logger = logging.getLogger(__package__)
17
18
19			class TargetNotFoundError(ValueError):
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
20			""""""
21
22
23			class TargetType(enum.Enum):
24			"""
25			Enum corresponding to the ChEMBL API field ``target.target_type``.
26			"""
27
28			single_protein = enum.auto()
29			protein_family = enum.auto()
30			protein_complex = enum.auto()
31			protein_complex_group = enum.auto()
32			selectivity_group = enum.auto()
33			protein_protein_interaction = enum.auto()
34			nucleic_acid = enum.auto()
35			chimeric_protein = enum.auto()
36			protein_nucleic_acid_complex = enum.auto()
37			metal = enum.auto()
38			small_molecule = enum.auto()
39			subcellular = enum.auto()
40			unknown = enum.auto()
41
42			@classmethod
43			def of(cls, s: str) -> TargetType:
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Method name "of" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Argument name "s" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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... introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
44			key = s.replace(" ", "_").replace("-", "_").lower()
45			try:
46			return TargetType[key]
47			except KeyError:
48			logger.error(f"Target type {key} not found. Using TargetType.unknown.")
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Use lazy % formatting in logging functions Loading history...
49			return TargetType.unknown
50
51			@classmethod
52			def protein_types(cls) -> Set[TargetType]:
53			"""
54			Returns the target types that are expressly proteins.
55			Specifically, single proteins, protein complexes, protein complex groups, and protein families.
			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 (103/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
56			This does not include protein-protein interactions, chimeric proteins,
57			protein-nucleic acid complexes, or selectivity groups.
58			"""
59			return {s for s in cls if s.is_protein}
60
61			@classmethod
62			def all_types(cls) -> Set[TargetType]:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
63			return set(TargetType) # here for symmetry
64
65			@property
66			def is_traversable(self) -> bool:
67			"""
68			Returns the target types that can have relationships defined on them.
69			Note that this may not match ChEMBL's own definition --
70			there may be types (e.g. protein_protein_interaction) that have relationships.
71			Those rare types are not included here.
72			"""
73			return self in {
74			TargetType.single_protein,
75			TargetType.protein_family,
76			TargetType.protein_complex,
77			TargetType.protein_complex_group,
78			TargetType.selectivity_group,
79			}
80
81			@property
82			def is_protein(self) -> bool:
83			"""
84			Whether this type is a "protein".
85			Specifically, single proteins, protein complexes, protein complex groups, and protein families.
			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 (103/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
86			This does not include protein-protein interactions, chimeric proteins,
87			protein-nucleic acid complexes, or selectivity groups.
88			"""
89			return self in {
90			TargetType.single_protein,
91			TargetType.protein_family,
92			TargetType.protein_complex,
93			TargetType.protein_complex_group,
94			}
95
96			@property
97			def is_unknown(self) -> bool:
98			"""
99			Returns whether this is the "unkown" type.
100			In principle, this could have a more involved meaning.
101			"""
102			return self == TargetType.unknown
103
104
105			@dataclass(frozen=True, order=True, repr=True)
106			class ChemblTarget:
107			"""
108			A target from ChEMBL, from the ``target`` table.
109
110			Attributes:
111			chembl: The CHEMBL ID, starting with 'CHEMBL'
112			name: The preferred name (``pref_target_name``)
113			type: From the ``target_type`` ChEMBL field
114			"""
115
116			chembl: str
117			name: Optional[str]
118			type: TargetType
119
120
121			class TargetFactory:
122			"""
123			Factory for ``Target`` that injects a ``ChemblApi``.
124			"""
125
126			def __init__(self, api: ChemblApi):
127			self.api = api
128
129			def find(self, chembl: str) -> ChemblTarget:
130			"""
131
132			Args:
133			chembl:
134
135			Returns:
136			A ``Target`` instance from a newly created subclass of that class
137			"""
138
139			try:
140			targets = self.api.target.filter(target_chembl_id=chembl)
141			except MaxRetryError:
142			raise TargetNotFoundError(f"Failed to find target {chembl}")
143			assert len(targets) == 1, f"Found {len(targets)} targets for {chembl}"
144			target = NestedDotDict(targets[0])
145			return ChemblTarget(
146			chembl=target["target_chembl_id"],
147			name=target.get("pref_name"),
148			type=TargetType.of(target["target_type"]),
149			)
150
151
152			__all__ = [
153			"TargetType",
154			"TargetFactory",
155			"TargetNotFoundError",
156			"ChemblTarget",
157			]
158

dmyersturnbull / mandos

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TargetFactory.__init__() A

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TargetFactory.init() A