mandos.search.chembl.target_traversal_strategy.TargetTraversalStrategy2.__call__() - Code Metrics - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

TargetTraversalStrategy2.call() C
last analyzed 2021-01-25 23:07 UTC

↳ Parent: mandos.search.chembl.target_traversal_strategy

Complexity

Conditions

Size

Total Lines	136
Code Lines	91

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	8
eloc	91
nop	2
dl	0
loc	136
rs	5.4278
c	0
b	0
f	0

How to fix Long Method

import abc

import sys
from typing import Sequence, Type

from mandos.chembl_api import ChemblApi
from mandos.model.targets import DagTargetLinkType, Target, TargetRelationshipType, TargetType


class TargetTraversalStrategy(metaclass=abc.ABCMeta):

    """"""

    @classmethod
    def api(cls) -> ChemblApi:

        raise NotImplementedError()

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

        return self.__call__(target)

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

        Returns:

        """
        raise NotImplementedError()


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

    """"""

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

        Returns:

        """
        return [target]


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

    """"""

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

        """
        edges = {
            DagTargetLinkType(
                TargetType.selectivity_group,
                TargetRelationshipType.superset_of,
                TargetType.protein_complex_group,
            ),
            DagTargetLinkType(
                TargetType.protein_complex_group,
                TargetRelationshipType.subset_of,
                TargetType.protein_complex_group,
            ),
            DagTargetLinkType(
                TargetType.selectivity_group,
                TargetRelationshipType.superset_of,
                TargetType.protein_family,
            ),
            DagTargetLinkType(
                TargetType.protein_family,
                TargetRelationshipType.subset_of,
                TargetType.protein_family,
            ),
        }
        found = target.traverse(edges)
        return [f.target for f in found if f.is_end]


class TargetTraversalStrategy2(TargetTraversalStrategy, metaclass=abc.ABCMeta):

    """"""

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

        Returns:

        """
        # 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
        if (
            target.type

            in [

                TargetType.single_protein,
                TargetType.protein_family,
                TargetType.protein_complex,
                TargetType.protein_complex_group,
            ]
            and ("subunit" in target.name.split(" ") or "chain" in target.name.split(" "))

        ):
            edges = {
                DagTargetLinkType(
                    TargetType.single_protein,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_complex,
                ),
                DagTargetLinkType(
                    TargetType.protein_complex,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_complex_group,
                ),
                DagTargetLinkType(
                    TargetType.protein_complex,
                    TargetRelationshipType.overlaps_with,
                    TargetType.protein_complex_group,
                ),
                DagTargetLinkType(
                    TargetType.protein_complex_group,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_complex_group,
                ),
                DagTargetLinkType(
                    TargetType.protein_complex_group,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_family,
                ),
                DagTargetLinkType(
                    TargetType.protein_family,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_family,
                ),
            }
        elif target.type in [TargetType.single_protein, TargetType.protein_family]:
            edges = {
                DagTargetLinkType(
                    TargetType.single_protein,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_family,
                ),
                DagTargetLinkType(
                    TargetType.protein_family,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_family,
                ),
            }
        elif target.type in [TargetType.protein_complex, TargetType.protein_complex_group]:
            edges = {
                DagTargetLinkType(
                    TargetType.protein_complex,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_complex_group,
                ),
                DagTargetLinkType(
                    TargetType.protein_complex,
                    TargetRelationshipType.overlaps_with,
                    TargetType.protein_complex_group,
                ),
                DagTargetLinkType(
                    TargetType.protein_complex_group,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_complex_group,
                ),
                DagTargetLinkType(
                    TargetType.protein_complex_group,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_family,
                ),
                DagTargetLinkType(
                    TargetType.protein_family,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_family,
                ),
            }
        elif target.type == TargetType.selectivity_group:
            edges = {
                DagTargetLinkType(
                    TargetType.selectivity_group,
                    TargetRelationshipType.superset_of,
                    TargetType.protein_complex_group,
                ),
                DagTargetLinkType(
                    TargetType.protein_complex_group,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_complex_group,
                ),
                DagTargetLinkType(
                    TargetType.selectivity_group,
                    TargetRelationshipType.superset_of,
                    TargetType.protein_family,
                ),
                DagTargetLinkType(
                    TargetType.protein_family,
                    TargetRelationshipType.subset_of,
                    TargetType.protein_family,
                ),
            }
        else:
            return [target]
        for edge in set(edges):
            edges.add(
                DagTargetLinkType(
                    edge.source_type, TargetRelationshipType.equivalent_to, edge.dest_type
                )
            )
        found = target.traverse(edges)
        return [f.target for f in found if f.is_end]


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			import abc
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2			import sys
3			from typing import Sequence, Type
4
5			from mandos.chembl_api import ChemblApi
6			from mandos.model.targets import DagTargetLinkType, Target, TargetRelationshipType, TargetType
7
8
9			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...
10			""""""
11
12			@classmethod
13			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...
14			raise NotImplementedError()
15
16			def traverse(self, target: Target) -> Sequence[Target]:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
17			return self.__call__(target)
18
19			def __call__(self, target: Target) -> Sequence[Target]:
20			"""
21
22			Returns:
23
24			"""
25			raise NotImplementedError()
26
27
28			class TargetTraversalStrategy0(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...
29			""""""
30
31			def __call__(self, target: Target) -> Sequence[Target]:
32			"""
33
34			Returns:
35
36			"""
37			return [target]
38
39
40			class TargetTraversalStrategy1(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...
41			""""""
42
43			def __call__(self, target: Target) -> Sequence[Target]:
44			"""
45			Returns:
46
47			"""
48			edges = {
49			DagTargetLinkType(
50			TargetType.selectivity_group,
51			TargetRelationshipType.superset_of,
52			TargetType.protein_complex_group,
53			),
54			DagTargetLinkType(
55			TargetType.protein_complex_group,
56			TargetRelationshipType.subset_of,
57			TargetType.protein_complex_group,
58			),
59			DagTargetLinkType(
60			TargetType.selectivity_group,
61			TargetRelationshipType.superset_of,
62			TargetType.protein_family,
63			),
64			DagTargetLinkType(
65			TargetType.protein_family,
66			TargetRelationshipType.subset_of,
67			TargetType.protein_family,
68			),
69			}
70			found = target.traverse(edges)
71			return [f.target for f in found if f.is_end]
72
73
74			class TargetTraversalStrategy2(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...
75			""""""
76
77			def __call__(self, target: Target) -> Sequence[Target]:
78			"""
79
80			Returns:
81
82			"""
83			# traverse the DAG up and down, following only desired links
84			# some links from complex to complex group are "overlaps with"
85			# ex: CHEMBL4296059
86			# it's also rare to need going from a selectivity group "down" to complex group / family / etc.
			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...
87			# usually they have a link upwards
88			# so...
89			# If it's a single protein, it's too risk to traverse up into complexes
90			# That's because lots of proteins occasionally make complexes, and there are some weird ones
			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 (102/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
91			# BUT We want to catch some obvious cases like GABA A subunits
92			# ChEMBL calls many of these "something subunit something"
93			# This is the only time we'll allow going directly from protein to complex
94			# In this case, we'll also disallow links form protein to family,
95			# just because we're pretty sure it's a subunit
96			# But we can go from single protein to complex to complex group to family
97			if (
98			target.type
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
99			in [
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
100			TargetType.single_protein,
101			TargetType.protein_family,
102			TargetType.protein_complex,
103			TargetType.protein_complex_group,
104			]
105			and ("subunit" in target.name.split(" ") or "chain" in target.name.split(" "))
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
106			):
107			edges = {
108			DagTargetLinkType(
109			TargetType.single_protein,
110			TargetRelationshipType.subset_of,
111			TargetType.protein_complex,
112			),
113			DagTargetLinkType(
114			TargetType.protein_complex,
115			TargetRelationshipType.subset_of,
116			TargetType.protein_complex_group,
117			),
118			DagTargetLinkType(
119			TargetType.protein_complex,
120			TargetRelationshipType.overlaps_with,
121			TargetType.protein_complex_group,
122			),
123			DagTargetLinkType(
124			TargetType.protein_complex_group,
125			TargetRelationshipType.subset_of,
126			TargetType.protein_complex_group,
127			),
128			DagTargetLinkType(
129			TargetType.protein_complex_group,
130			TargetRelationshipType.subset_of,
131			TargetType.protein_family,
132			),
133			DagTargetLinkType(
134			TargetType.protein_family,
135			TargetRelationshipType.subset_of,
136			TargetType.protein_family,
137			),
138			}
139			elif target.type in [TargetType.single_protein, TargetType.protein_family]:
140			edges = {
141			DagTargetLinkType(
142			TargetType.single_protein,
143			TargetRelationshipType.subset_of,
144			TargetType.protein_family,
145			),
146			DagTargetLinkType(
147			TargetType.protein_family,
148			TargetRelationshipType.subset_of,
149			TargetType.protein_family,
150			),
151			}
152			elif target.type in [TargetType.protein_complex, TargetType.protein_complex_group]:
153			edges = {
154			DagTargetLinkType(
155			TargetType.protein_complex,
156			TargetRelationshipType.subset_of,
157			TargetType.protein_complex_group,
158			),
159			DagTargetLinkType(
160			TargetType.protein_complex,
161			TargetRelationshipType.overlaps_with,
162			TargetType.protein_complex_group,
163			),
164			DagTargetLinkType(
165			TargetType.protein_complex_group,
166			TargetRelationshipType.subset_of,
167			TargetType.protein_complex_group,
168			),
169			DagTargetLinkType(
170			TargetType.protein_complex_group,
171			TargetRelationshipType.subset_of,
172			TargetType.protein_family,
173			),
174			DagTargetLinkType(
175			TargetType.protein_family,
176			TargetRelationshipType.subset_of,
177			TargetType.protein_family,
178			),
179			}
180			elif target.type == TargetType.selectivity_group:
181			edges = {
182			DagTargetLinkType(
183			TargetType.selectivity_group,
184			TargetRelationshipType.superset_of,
185			TargetType.protein_complex_group,
186			),
187			DagTargetLinkType(
188			TargetType.protein_complex_group,
189			TargetRelationshipType.subset_of,
190			TargetType.protein_complex_group,
191			),
192			DagTargetLinkType(
193			TargetType.selectivity_group,
194			TargetRelationshipType.superset_of,
195			TargetType.protein_family,
196			),
197			DagTargetLinkType(
198			TargetType.protein_family,
199			TargetRelationshipType.subset_of,
200			TargetType.protein_family,
201			),
202			}
203			else:
204			return [target]
205			for edge in set(edges):
206			edges.add(
207			DagTargetLinkType(
208			edge.source_type, TargetRelationshipType.equivalent_to, edge.dest_type
209			)
210			)
211			found = target.traverse(edges)
212			return [f.target for f in found if f.is_end]
213
214
215			class TargetTraversalStrategies:
216			"""
217			Factory.
218			"""
219
220			@classmethod
221			def by_name(cls, fully_qualified: str, api: ChemblApi) -> TargetTraversalStrategy:
222			"""
223			For dependency injection.
224
225			Args:
226			fully_qualified:
227			api:
228
229			Returns:
230
231			"""
232			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]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
233			mod = s[: s.rfind(".")]
234			clz = s[s.rfind(".") :]
235			x = getattr(sys.modules[mod], clz)
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
236			return cls.create(x, api)
237
238			@classmethod
239			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...
240			return cls.create(TargetTraversalStrategy0, api)
241
242			@classmethod
243			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...
244			return cls.create(TargetTraversalStrategy1, api)
245
246			@classmethod
247			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...
248			return cls.create(TargetTraversalStrategy2, api)
249
250			@classmethod
251			def create(cls, clz: Type[TargetTraversalStrategy], api: ChemblApi) -> TargetTraversalStrategy:
252			"""
253			Factory method.
254
255			Args:
256			clz:
257			api:
258
259			Returns:
260
261			"""
262
263			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 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
264			@classmethod
265			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...
266			return api
267
268			X.__name__ = clz.__name__
269			return X()
270
271
272			__all__ = ["TargetTraversalStrategy", "TargetTraversalStrategies"]
273

dmyersturnbull / mandos

TargetTraversalStrategy2.__call__() C last analyzed 2021-01-25 23:07 UTC

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TargetTraversalStrategy2.call() C
last analyzed 2021-01-25 23:07 UTC