mandos.search.chembl.target_traversal.StandardStrategyParser.parse() - Code Metrics - Inspection of "feat: improve cli and readme" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( 1f8603...9ff912 )

by Douglas

created 2021-03-16 18:38 UTC

StandardStrategyParser.parse() C

↳ Parent: mandos.search.chembl.target_traversal

Complexity

Conditions

Size

Total Lines	63
Code Lines	57

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	10
eloc	57
nop	2
dl	0
loc	63
rs	5.6072
c	0
b	0
f	0

How to fix Long Method Complexity

Long Method

Small methods make your code easier to understand, in particular if combined with a good name. Besides, if your method is small, finding a good name is usually much easier.

For example, if you find yourself adding comments to a method's body, this is usually a good sign to extract the commented part to a new method, and use the comment as a starting point when coming up with a good name for this new method.

Commonly applied refactorings include:

If many parameters/temporary variables are present:
- Replace temporary variables with Query
- Introduce parameter object; often combined with preserve whole object
- If the above two are insufficient: Replace method with method object
If you have long conditionals: Decompose Conditional
Otherwise: Extract method

Complexity

Complex classes like mandos.search.chembl.target_traversal.StandardStrategyParser.parse() often do a lot of different things. To break such a class down, we need to identify a cohesive component within that class. A common approach to find such a component is to look for fields/methods that share the same prefixes, or suffixes.

Once you have determined the fields that belong together, you can apply the Extract Class refactoring. If the component makes sense as a sub-class, Extract Subclass is also a candidate, and is often faster.

from __future__ import annotations

import abc
import enum
import sys
import sre_compile
import re
from pathlib import Path
from typing import Dict, Sequence, Type, Set, Optional, Mapping
from typing import Tuple as Tup

from mandos.model import MandosResources
from mandos.model.chembl_api import ChemblApi
from mandos.model.chembl_support.chembl_targets import TargetType, ChemblTarget
from mandos.model.chembl_support.chembl_target_graphs import (
    ChemblTargetGraph,
    TargetNode,
    TargetEdgeReqs,
    TargetRelType,
)


class Acceptance(enum.Enum):

    always = enum.auto()
    never = enum.auto()
    at_start = enum.auto()
    at_end = enum.auto()


class TargetTraversalStrategy(metaclass=abc.ABCMeta):

    """"""

    @classmethod
    def api(cls) -> ChemblApi:

        raise NotImplementedError()

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

        return self.__call__(target)

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

        Returns:

        """
        raise NotImplementedError()


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

    """"""

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

        raise NotImplementedError()

    @classmethod
    @property
    def acceptance(cls) -> Mapping[TargetEdgeReqs, Acceptance]:

        raise NotImplementedError()

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

    def accept(self, target: TargetNode) -> bool:

        acceptance_type = self.acceptance[target.link_reqs]
        return (
            acceptance_type is Acceptance.always
            or (acceptance_type is Acceptance.at_start and target.is_start)
            or (acceptance_type is Acceptance.at_end and target.is_end)
        )


class StandardStrategyParser:

    @classmethod
    def read_lines(cls, path: Path) -> Sequence[str]:

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

    @classmethod
    def parse(

        cls, lines: Sequence[str]

    ) -> Tup[Set[TargetEdgeReqs], Mapping[TargetEdgeReqs, Acceptance]]:
        pat_type = r"([a-z_]+)"
        pat_rel = r"([<>~=])"
        pat_accept = r"(?:accept:([\-*^$]?))?"
        pat_src_words = r"(?:src:'''(.+?)''')?"
        pat_dest_words = r"(?:dest:'''(.+?)''')?"
        comment = r"(?:#(.*))?"
        pat = f"^ *{pat_type} *{pat_rel} *{pat_type} *{pat_accept} * {pat_src_words} *{pat_dest_words} *{comment} *$"

        pat = re.compile(pat)
        to_rel = {
            ">": TargetRelType.superset_of,
            "<": TargetRelType.subset_of,
            "~": TargetRelType.overlaps_with,
            "=": TargetRelType.equivalent_to,
            "*": TargetRelType.any_link,
            ".": TargetRelType.self_link,
        }
        to_accept = {
            "*": Acceptance.always,
            "-": Acceptance.never,
            "^": Acceptance.at_start,
            "$": Acceptance.at_end,
        }
        edges = set()
        edge_to_acceptance: Dict[TargetEdgeReqs, Acceptance] = {}
        for line in lines:
            match = pat.fullmatch(line)
            if match is None:
                raise AssertionError(f"Could not parse line '{line}'")
            try:
                src_str = match.group(1).lower()
                sources = TargetType.all_types() if src_str == "any" else [TargetType[src_str]]
                rel = to_rel[match.group(2)]
                dest_str = match.group(3).lower()
                targets = TargetType.all_types() if dest_str == "any" else [TargetType[dest_str]]
                accept = to_accept[match.group(4).lower()]
                src_pat = (
                    None
                    if match.group(5) is None or match.group(5) == ""
                    else re.compile(match.group(5))
                )
                dest_pat = (
                    None
                    if match.group(6) is None or match.group(6) == ""
                    else re.compile(match.group(6))
                )
            except (KeyError, TypeError, sre_compile.error):
                raise AssertionError(f"Could not parse line '{line}'")
            for source in sources:
                for dest in targets:
                    edge = TargetEdgeReqs(
                        src_type=source,
                        src_pattern=src_pat,
                        rel_type=rel,
                        dest_type=dest,
                        dest_pattern=dest_pat,
                    )
                    edges.add(edge)
                    edge_to_acceptance[edge] = accept
        return edges, edge_to_acceptance


class TargetTraversalStrategies:
    """
    Factory.
    """

    @classmethod
    def by_name(cls, name: str, api: ChemblApi) -> TargetTraversalStrategy:

        if MandosResources.contains("strategies", name, suffix=".strat"):

            return cls.from_resource(name, api)
        elif name.endswith(".strat"):
            return cls.from_file(Path(name), api)
        return cls.by_classname(name, api)

    @classmethod
    def by_classname(cls, fully_qualified: str, api: ChemblApi) -> TargetTraversalStrategy:

        s = fully_qualified

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

        except AttributeError:
            raise LookupError(
                f"Did not find strategy by fully-qualified class name {fully_qualified}"
            )
        return cls.create(x, api)

    @classmethod
    def from_resource(cls, name: str, api: ChemblApi) -> TargetTraversalStrategy:

        path = MandosResources.path("strategies", name)
        lines = StandardStrategyParser.read_lines(path)
        return cls._from_lines(lines, api, path.stem)

    @classmethod
    def from_file(cls, path: Path, api: ChemblApi) -> TargetTraversalStrategy:

        lines = StandardStrategyParser.read_lines(path)
        return cls._from_lines(lines, api, path.stem)

    @classmethod
    def from_lines(

        cls, lines: Sequence[str], api: ChemblApi, name: Optional[str]

    ) -> TargetTraversalStrategy:
        return cls._from_lines(lines, api, "" if name is None else name)

    @classmethod
    def _from_lines(
        cls, lines: Sequence[str], api: ChemblApi, name: str

    ) -> TargetTraversalStrategy:
        edges, accept = StandardStrategyParser.parse(lines)

        class Strategy(StandardTargetTraversalStrategy):

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

                return edges

            @classmethod
            def acceptance(cls) -> Mapping[TargetEdgeReqs, Acceptance]:

                return accept

            @classmethod
            def api(cls) -> ChemblApi:
                return api

        Strategy.__name__ = StandardTargetTraversalStrategy.__class__.__name__ + "_" + name
        return Strategy()

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

        return cls.from_resource("null.txt", api)

    # noinspection PyAbstractClass
    @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 enum
4			import sys
5			import sre_compile
6			import re
7			from pathlib import Path
8			from typing import Dict, Sequence, Type, Set, Optional, Mapping
9			from typing import Tuple as Tup
10
11			from mandos.model import MandosResources
12			from mandos.model.chembl_api import ChemblApi
13			from mandos.model.chembl_support.chembl_targets import TargetType, ChemblTarget
14			from mandos.model.chembl_support.chembl_target_graphs import (
15			ChemblTargetGraph,
16			TargetNode,
17			TargetEdgeReqs,
18			TargetRelType,
19			)
20
21
22			class Acceptance(enum.Enum):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
23			always = enum.auto()
24			never = enum.auto()
25			at_start = enum.auto()
26			at_end = enum.auto()
27
28
29			class TargetTraversalStrategy(metaclass=abc.ABCMeta):
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30			""""""
31
32			@classmethod
33			def api(cls) -> ChemblApi:
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34			raise NotImplementedError()
35
36			def traverse(self, target: ChemblTargetGraph) -> Sequence[ChemblTargetGraph]:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
37			return self.__call__(target)
38
39			def __call__(self, target: ChemblTargetGraph) -> Sequence[ChemblTargetGraph]:
40			"""
41
42			Returns:
43
44			"""
45			raise NotImplementedError()
46
47
48			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...
49			""""""
50
51			@classmethod
52			@property
53			def edges(cls) -> Set[TargetEdgeReqs]:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
54			raise NotImplementedError()
55
56			@classmethod
57			@property
58			def acceptance(cls) -> Mapping[TargetEdgeReqs, Acceptance]:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
59			raise NotImplementedError()
60
61			def __call__(self, target: ChemblTargetGraph) -> Sequence[ChemblTarget]:
62			if not target.type.is_traversable:
63			return [target.target]
64			found = target.traverse(self.edges)
65			return [f.target for f in found if self.accept(f)]
66
67			def accept(self, target: TargetNode) -> bool:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
68			acceptance_type = self.acceptance[target.link_reqs]
69			return (
70			acceptance_type is Acceptance.always
71			or (acceptance_type is Acceptance.at_start and target.is_start)
72			or (acceptance_type is Acceptance.at_end and target.is_end)
73			)
74
75
76			class StandardStrategyParser:
			0 ignored issues – show introduced 2021-03-13 01:12 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
77			@classmethod
78			def read_lines(cls, path: Path) -> Sequence[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...
79			return [
80			line
81			for line in path.read_text(encoding="utf8").splitlines()
82			if not line.startswith("#") and len(line.strip()) > 0
83			]
84
85			@classmethod
86			def parse(
			0 ignored issues – show Comprehensibility introduced 2021-03-13 01:12 UTC by Report Bug Copy Issue Report This function exceeds the maximum number of variables (26/15). Loading history... introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
87			cls, lines: Sequence[str]
			0 ignored issues – show Coding Style introduced 2021-03-15 02:29 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
88			) -> Tup[Set[TargetEdgeReqs], Mapping[TargetEdgeReqs, Acceptance]]:
89			pat_type = r"([a-z_]+)"
90			pat_rel = r"([<>~=])"
91			pat_accept = r"(?:accept:([\-*^$]?))?"
92			pat_src_words = r"(?:src:'''(.+?)''')?"
93			pat_dest_words = r"(?:dest:'''(.+?)''')?"
94			comment = r"(?:#(.*))?"
95			pat = f"^ {pat_type} {pat_rel} {pat_type} {pat_accept} * {pat_src_words} {pat_dest_words} {comment} *$"
			0 ignored issues – show Coding Style introduced 2021-03-13 01:12 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (117/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
96			pat = re.compile(pat)
97			to_rel = {
98			">": TargetRelType.superset_of,
99			"<": TargetRelType.subset_of,
100			"~": TargetRelType.overlaps_with,
101			"=": TargetRelType.equivalent_to,
102			"*": TargetRelType.any_link,
103			".": TargetRelType.self_link,
104			}
105			to_accept = {
106			"*": Acceptance.always,
107			"-": Acceptance.never,
108			"^": Acceptance.at_start,
109			"$": Acceptance.at_end,
110			}
111			edges = set()
112			edge_to_acceptance: Dict[TargetEdgeReqs, Acceptance] = {}
113			for line in lines:
114			match = pat.fullmatch(line)
115			if match is None:
116			raise AssertionError(f"Could not parse line '{line}'")
117			try:
118			src_str = match.group(1).lower()
119			sources = TargetType.all_types() if src_str == "any" else [TargetType[src_str]]
120			rel = to_rel[match.group(2)]
121			dest_str = match.group(3).lower()
122			targets = TargetType.all_types() if dest_str == "any" else [TargetType[dest_str]]
123			accept = to_accept[match.group(4).lower()]
124			src_pat = (
125			None
126			if match.group(5) is None or match.group(5) == ""
127			else re.compile(match.group(5))
128			)
129			dest_pat = (
130			None
131			if match.group(6) is None or match.group(6) == ""
132			else re.compile(match.group(6))
133			)
134			except (KeyError, TypeError, sre_compile.error):
135			raise AssertionError(f"Could not parse line '{line}'")
136			for source in sources:
137			for dest in targets:
138			edge = TargetEdgeReqs(
139			src_type=source,
140			src_pattern=src_pat,
141			rel_type=rel,
142			dest_type=dest,
143			dest_pattern=dest_pat,
144			)
145			edges.add(edge)
146			edge_to_acceptance[edge] = accept
147			return edges, edge_to_acceptance
148
149
150			class TargetTraversalStrategies:
151			"""
152			Factory.
153			"""
154
155			@classmethod
156			def by_name(cls, name: str, 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...
157			if MandosResources.contains("strategies", name, suffix=".strat"):
			0 ignored issues – show unused-code introduced 2021-03-16 18:40 UTC by Report Bug Copy Issue Report Unnecessary "elif" after "return" Loading history...
158			return cls.from_resource(name, api)
159			elif name.endswith(".strat"):
160			return cls.from_file(Path(name), api)
161			return cls.by_classname(name, api)
162
163			@classmethod
164			def by_classname(cls, fully_qualified: str, 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...
165			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...
166			mod = s[: s.rfind(".")]
167			clz = s[s.rfind(".") :]
168			try:
169			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...
170			except AttributeError:
171			raise LookupError(
172			f"Did not find strategy by fully-qualified class name {fully_qualified}"
173			)
174			return cls.create(x, api)
175
176			@classmethod
177			def from_resource(cls, name: str, api: ChemblApi) -> TargetTraversalStrategy:
			0 ignored issues – show introduced 2021-03-13 01:12 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
178			path = MandosResources.path("strategies", name)
179			lines = StandardStrategyParser.read_lines(path)
180			return cls._from_lines(lines, api, path.stem)
181
182			@classmethod
183			def from_file(cls, path: Path, api: ChemblApi) -> TargetTraversalStrategy:
			0 ignored issues – show introduced 2021-03-13 01:12 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
184			lines = StandardStrategyParser.read_lines(path)
185			return cls._from_lines(lines, api, path.stem)
186
187			@classmethod
188			def from_lines(
			0 ignored issues – show introduced 2021-03-15 02:29 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
189			cls, lines: Sequence[str], api: ChemblApi, name: Optional[str]
			0 ignored issues – show Coding Style introduced 2021-03-15 02:29 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
190			) -> TargetTraversalStrategy:
191			return cls._from_lines(lines, api, "" if name is None else name)
192
193			@classmethod
194			def _from_lines(
195			cls, lines: Sequence[str], api: ChemblApi, name: str
			0 ignored issues – show Coding Style introduced 2021-03-15 02:29 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
196			) -> TargetTraversalStrategy:
197			edges, accept = StandardStrategyParser.parse(lines)
198
199			class Strategy(StandardTargetTraversalStrategy):
			0 ignored issues – show introduced 2021-03-15 02:29 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
200			@classmethod
201			def edges(cls) -> Set[TargetEdgeReqs]:
			0 ignored issues – show introduced 2021-03-15 02:29 UTC by Report Bug Copy Issue Report Method 'edges' was expected to be 'property', found it instead as 'classmethod' Loading history...
202			return edges
203
204			@classmethod
205			def acceptance(cls) -> Mapping[TargetEdgeReqs, Acceptance]:
			0 ignored issues – show introduced 2021-03-15 02:29 UTC by Report Bug Copy Issue Report Method 'acceptance' was expected to be 'property', found it instead as 'classmethod' Loading history...
206			return accept
207
208			@classmethod
209			def api(cls) -> ChemblApi:
210			return api
211
212			Strategy.__name__ = StandardTargetTraversalStrategy.__class__.__name__ + "_" + name
213			return Strategy()
214
215			@classmethod
216			def null(cls, api: ChemblApi) -> TargetTraversalStrategy:
			0 ignored issues – show introduced 2021-03-16 18:40 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
217			return cls.from_resource("null.txt", api)
218
219			# noinspection PyAbstractClass
220			@classmethod
221			def create(cls, clz: Type[TargetTraversalStrategy], api: ChemblApi) -> TargetTraversalStrategy:
222			"""
223			Factory method.
224
225			Args:
226			clz:
227			api:
228
229			Returns:
230
231			"""
232
233			class X(clz):
			0 ignored issues – show 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... introduced 2021-03-15 02:29 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
234			@classmethod
235			def api(cls) -> ChemblApi:
			0 ignored issues – show introduced 2021-03-16 18:40 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
236			return api
237
238			X.__name__ = clz.__name__
239			return X()
240
241
242			__all__ = ["TargetTraversalStrategy", "TargetTraversalStrategies"]
243

dmyersturnbull / mandos

Push — main ( 1f8603...9ff912 )

StandardStrategyParser.parse() C

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