mandos.search.chembl.target_traversal.TargetTraversalStrategies.strategy2() - Code Metrics - Inspection of "feat: major refactoring" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( bfa577...eb6882 )

by Douglas

created 2021-03-10 02:36 UTC

TargetTraversalStrategies.strategy2() A

↳ Parent: mandos.search.chembl.target_traversal

Complexity

Conditions

Size

Total Lines	3
Code Lines	3

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	3
nop	2
dl	0
loc	3
rs	10
c	0
b	0
f	0

from __future__ import annotations

import abc
import sys
import re
from pathlib import Path
from typing import Sequence, Type, Set

from mandos.model import MandosResources
from mandos.model.chembl_api import ChemblApi
from mandos.model.chembl_support.chembl_targets import (
    DagTargetLinkType,
    ChemblTarget,
    TargetRelationshipType,
    TargetType,
)


class TargetTraversalStrategy(metaclass=abc.ABCMeta):

    """"""

    @classmethod
    def api(cls) -> ChemblApi:

        raise NotImplementedError()

    def traverse(self, target: ChemblTarget) -> Sequence[ChemblTarget]:

        return self.__call__(target)

    def __call__(self, target: ChemblTarget) -> Sequence[ChemblTarget]:
        """

        Returns:

        """
        raise NotImplementedError()


class StandardTargetTraversalStrategy(TargetTraversalStrategy, metaclass=abc.ABCMeta):

    """"""

    @classmethod
    def edges(cls) -> Set[DagTargetLinkType]:

        raise NotImplementedError()

    @classmethod
    def read(cls, path: Path) -> Set[DagTargetLinkType]:

        lines = [
            line
            for line in path.read_text(encoding="utf8").splitlines()
            if not line.startswith("#") and len(line.strip()) > 0
        ]
        return cls.parse(lines)

    @classmethod
    def parse(cls, lines: Sequence[str]) -> Set[DagTargetLinkType]:

        pat_type = re.compile(r"([a-z_]+)")
        pat_rel = re.compile(r"((?:->)|(?:<-)|(?:==)|(?:~~))")
        pat_words = re.compile(r"(?:words: *([^|]+(?:\|[^|]+)+))?")
        pat = re.compile(f"^ *{pat_type} *{pat_rel} *{pat_type} *{pat_words} *$")
        to_rel = {
            "->": TargetRelationshipType.superset_of,
            "<-": TargetRelationshipType.subset_of,
            "~~": TargetRelationshipType.overlaps_with,
            "==": TargetRelationshipType.equivalent_to,
        }
        edges = set()
        for line in lines:
            match = pat.fullmatch(line)
            if match is None:
                raise AssertionError(f"Could not parse line '{line}'")
            try:
                source = TargetType[match.group(1).lower()]
                rel = TargetRelationshipType[to_rel[match.group(2).lower()]]
                target = TargetType[match.group(3).lower()]
                words = None if match.group(4) == "" else match.group(4).split("|")
            except KeyError:
                raise AssertionError(f"Could not parse line '{line}'")
            edges.add(DagTargetLinkType(source, rel, target, words))
        return edges

    def __call__(self, target: ChemblTarget) -> Sequence[ChemblTarget]:
        """
        Returns:
        """
        if not target.type.is_traversable:
            return [target]
        found = target.traverse(self.edges)
        return [f.target for f in found if f.is_end]


class TargetTraversalStrategy0(StandardTargetTraversalStrategy, metaclass=abc.ABCMeta):

    """"""

    @classmethod
    def edges(cls) -> Set[DagTargetLinkType]:
        return cls.read(MandosResources.path("strategies", "strategy0.txt"))


class TargetTraversalStrategy1(StandardTargetTraversalStrategy, metaclass=abc.ABCMeta):

    """"""

    @classmethod
    def edges(cls) -> Set[DagTargetLinkType]:
        return cls.read(MandosResources.path("strategies", "strategy1.txt"))


class TargetTraversalStrategy2(StandardTargetTraversalStrategy, metaclass=abc.ABCMeta):
    """
    Traverse the DAG up and down, following only desired links
    Some links from complex to complex group are "overlaps with"
    ex: CHEMBL4296059
    it's also rare to need going from a selectivity group "down" to complex group / family / etc.
    usually they have a link upwards
    so...
    If it's a single protein, it's too risk to traverse up into complexes
    That's because lots of proteins *occasionally* make complexes, and there are some weird ones
    BUT We want to catch some obvious cases like GABA A subunits
    ChEMBL calls many of these "something subunit something"
    This is the only time we'll allow going directly from protein to complex
    In this case, we'll also disallow links form protein to family,
    just because we're pretty sure it's a subunit
    But we can go from single protein to complex to complex group to family
    """

    @classmethod
    def edges(cls) -> Set[DagTargetLinkType]:
        return cls.read(MandosResources.path("strategies", "strategy2.txt"))


class TargetTraversalStrategies:
    """
    Factory.
    """

    @classmethod
    def by_name(cls, fully_qualified: str, api: ChemblApi) -> TargetTraversalStrategy:
        """
        For dependency injection.

        Args:
            fully_qualified:
            api:

        Returns:

        """
        s = fully_qualified

        mod = s[: s.rfind(".")]
        clz = s[s.rfind(".") :]
        x = getattr(sys.modules[mod], clz)

        return cls.create(x, api)

    @classmethod
    def strategy0(cls, api: ChemblApi) -> TargetTraversalStrategy:

        return cls.create(TargetTraversalStrategy0, api)

    @classmethod
    def strategy1(cls, api: ChemblApi) -> TargetTraversalStrategy:

        return cls.create(TargetTraversalStrategy1, api)

    @classmethod
    def strategy2(cls, api: ChemblApi) -> TargetTraversalStrategy:

        return cls.create(TargetTraversalStrategy2, api)

    @classmethod
    def create(cls, clz: Type[TargetTraversalStrategy], api: ChemblApi) -> TargetTraversalStrategy:
        """
        Factory method.

        Args:
            clz:
            api:

        Returns:

        """

        class X(clz):

            @classmethod
            def api(cls) -> ChemblApi:

                return api

        X.__name__ = clz.__name__
        return X()


__all__ = ["TargetTraversalStrategy", "TargetTraversalStrategies"]


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			import abc
3			import sys
4			import re
5			from pathlib import Path
6			from typing import Sequence, Type, Set
7
8			from mandos.model import MandosResources
9			from mandos.model.chembl_api import ChemblApi
10			from mandos.model.chembl_support.chembl_targets import (
11			DagTargetLinkType,
12			ChemblTarget,
13			TargetRelationshipType,
14			TargetType,
15			)
16
17
18			class TargetTraversalStrategy(metaclass=abc.ABCMeta):
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
19			""""""
20
21			@classmethod
22			def api(cls) -> ChemblApi:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
23			raise NotImplementedError()
24
25			def traverse(self, target: ChemblTarget) -> Sequence[ChemblTarget]:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
26			return self.__call__(target)
27
28			def __call__(self, target: ChemblTarget) -> Sequence[ChemblTarget]:
29			"""
30
31			Returns:
32
33			"""
34			raise NotImplementedError()
35
36
37			class StandardTargetTraversalStrategy(TargetTraversalStrategy, metaclass=abc.ABCMeta):
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
38			""""""
39
40			@classmethod
41			def edges(cls) -> Set[DagTargetLinkType]:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
42			raise NotImplementedError()
43
44			@classmethod
45			def read(cls, path: Path) -> Set[DagTargetLinkType]:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
46			lines = [
47			line
48			for line in path.read_text(encoding="utf8").splitlines()
49			if not line.startswith("#") and len(line.strip()) > 0
50			]
51			return cls.parse(lines)
52
53			@classmethod
54			def parse(cls, lines: Sequence[str]) -> Set[DagTargetLinkType]:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
55			pat_type = re.compile(r"([a-z_]+)")
56			pat_rel = re.compile(r"((?:->)\|(?:<-)\|(?:==)\|(?:~~))")
57			pat_words = re.compile(r"(?:words: *([^\|]+(?:\\|[^\|]+)+))?")
58			pat = re.compile(f"^ {pat_type} {pat_rel} {pat_type} {pat_words} *$")
59			to_rel = {
60			"->": TargetRelationshipType.superset_of,
61			"<-": TargetRelationshipType.subset_of,
62			"~~": TargetRelationshipType.overlaps_with,
63			"==": TargetRelationshipType.equivalent_to,
64			}
65			edges = set()
66			for line in lines:
67			match = pat.fullmatch(line)
68			if match is None:
69			raise AssertionError(f"Could not parse line '{line}'")
70			try:
71			source = TargetType[match.group(1).lower()]
72			rel = TargetRelationshipType[to_rel[match.group(2).lower()]]
73			target = TargetType[match.group(3).lower()]
74			words = None if match.group(4) == "" else match.group(4).split("\|")
75			except KeyError:
76			raise AssertionError(f"Could not parse line '{line}'")
77			edges.add(DagTargetLinkType(source, rel, target, words))
78			return edges
79
80			def __call__(self, target: ChemblTarget) -> Sequence[ChemblTarget]:
81			"""
82			Returns:
83			"""
84			if not target.type.is_traversable:
85			return [target]
86			found = target.traverse(self.edges)
87			return [f.target for f in found if f.is_end]
88
89
90			class TargetTraversalStrategy0(StandardTargetTraversalStrategy, metaclass=abc.ABCMeta):
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
91			""""""
92
93			@classmethod
94			def edges(cls) -> Set[DagTargetLinkType]:
95			return cls.read(MandosResources.path("strategies", "strategy0.txt"))
96
97
98			class TargetTraversalStrategy1(StandardTargetTraversalStrategy, metaclass=abc.ABCMeta):
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
99			""""""
100
101			@classmethod
102			def edges(cls) -> Set[DagTargetLinkType]:
103			return cls.read(MandosResources.path("strategies", "strategy1.txt"))
104
105
106			class TargetTraversalStrategy2(StandardTargetTraversalStrategy, metaclass=abc.ABCMeta):
107			"""
108			Traverse the DAG up and down, following only desired links
109			Some links from complex to complex group are "overlaps with"
110			ex: CHEMBL4296059
111			it's also rare to need going from a selectivity group "down" to complex group / family / etc.
112			usually they have a link upwards
113			so...
114			If it's a single protein, it's too risk to traverse up into complexes
115			That's because lots of proteins occasionally make complexes, and there are some weird ones
116			BUT We want to catch some obvious cases like GABA A subunits
117			ChEMBL calls many of these "something subunit something"
118			This is the only time we'll allow going directly from protein to complex
119			In this case, we'll also disallow links form protein to family,
120			just because we're pretty sure it's a subunit
121			But we can go from single protein to complex to complex group to family
122			"""
123
124			@classmethod
125			def edges(cls) -> Set[DagTargetLinkType]:
126			return cls.read(MandosResources.path("strategies", "strategy2.txt"))
127
128
129			class TargetTraversalStrategies:
130			"""
131			Factory.
132			"""
133
134			@classmethod
135			def by_name(cls, fully_qualified: str, api: ChemblApi) -> TargetTraversalStrategy:
136			"""
137			For dependency injection.
138
139			Args:
140			fully_qualified:
141			api:
142
143			Returns:
144
145			"""
146			s = fully_qualified
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable 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...
147			mod = s[: s.rfind(".")]
148			clz = s[s.rfind(".") :]
149			x = getattr(sys.modules[mod], clz)
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
150			return cls.create(x, api)
151
152			@classmethod
153			def strategy0(cls, api: ChemblApi) -> TargetTraversalStrategy:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
154			return cls.create(TargetTraversalStrategy0, api)
155
156			@classmethod
157			def strategy1(cls, api: ChemblApi) -> TargetTraversalStrategy:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
158			return cls.create(TargetTraversalStrategy1, api)
159
160			@classmethod
161			def strategy2(cls, api: ChemblApi) -> TargetTraversalStrategy:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
162			return cls.create(TargetTraversalStrategy2, api)
163
164			@classmethod
165			def create(cls, clz: Type[TargetTraversalStrategy], api: ChemblApi) -> TargetTraversalStrategy:
166			"""
167			Factory method.
168
169			Args:
170			clz:
171			api:
172
173			Returns:
174
175			"""
176
177			class X(clz):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing class docstring Loading history... Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Class name "X" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' 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			@classmethod
179			def api(cls) -> ChemblApi:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
180			return api
181
182			X.__name__ = clz.__name__
183			return X()
184
185
186			__all__ = ["TargetTraversalStrategy", "TargetTraversalStrategies"]
187

dmyersturnbull / mandos

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TargetTraversalStrategies.strategy2() A

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