mandos.search.pubchem.drugbank_interaction_search.DrugbankTargetSearch._get_predicate() - Code Metrics - Inspection of "feat: improve predicate/source distinction" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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by Douglas

created 2021-04-04 05:54 UTC

DrugbankTargetSearch._get_predicate() A

↳ Parent: mandos.search.pubchem.drugbank_interaction_search

Complexity

Conditions

Size

Total Lines	3
Code Lines	3

Duplication

Lines	0
Ratio	0 %

Importance

Changes

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

from dataclasses import dataclass

from typing import Sequence, TypeVar, Set

from mandos.model.pubchem_api import PubchemApi
from mandos.model.pubchem_support.pubchem_models import DrugbankTargetType, DrugbankInteraction
from mandos.search.pubchem import PubchemHit, PubchemSearch


@dataclass(frozen=True, order=True, repr=True)
class _DrugbankInteractionHit(PubchemHit):
    """"""

    gene_symbol: str
    protein_id: str
    target_type: str
    target_name: str
    general_function: str


@dataclass(frozen=True, order=True, repr=True)

class DrugbankTargetHit(_DrugbankInteractionHit):
    """"""


@dataclass(frozen=True, order=True, repr=True)

class DrugbankGeneralFunctionHit(_DrugbankInteractionHit):
    """"""


T = TypeVar("T", bound=_DrugbankInteractionHit, covariant=True)



class _DrugbankInteractionSearch(PubchemSearch[T]):
    def __init__(self, key: str, api: PubchemApi, target_types: Set[DrugbankTargetType]):
        super().__init__(key, api)
        self.target_types = target_types

    """"""


    @classmethod
    def _get_obj(cls, dd: DrugbankInteraction) -> str:

        raise NotImplementedError()

    @classmethod
    def _get_predicate(cls, dd: DrugbankInteraction) -> str:

        raise NotImplementedError()

    def find(self, inchikey: str) -> Sequence[T]:

        data = self.api.fetch_data(inchikey)
        # noinspection PyPep8Naming
        H = self.__class__.get_h()

        return [
            H(
                record_id=dd.record_id,
                origin_inchikey=inchikey,
                matched_inchikey=data.names_and_identifiers.inchikey,
                compound_id=str(data.cid),
                compound_name=data.name,
                predicate=self._get_predicate(dd),
                object_id=self._get_obj(dd),
                object_name=self._get_obj(dd),
                search_key=self.key,
                search_class=self.search_class,
                data_source=self.data_source,
                gene_symbol=dd.gene_symbol,
                protein_id=dd.protein_id,
                target_type=dd.target_type.name,
                target_name=dd.target_name,
                general_function=dd.general_function,
            )
            for dd in data.biomolecular_interactions_and_pathways.drugbank_interactions
            if dd.target_type in self.target_types
        ]


class DrugbankTargetSearch(_DrugbankInteractionSearch[_DrugbankInteractionHit]):

    """"""

    @property
    def data_source(self) -> str:

        return "DrugBank :: target interactions"

    @classmethod
    def _get_obj(cls, dd: DrugbankInteraction) -> str:

        return dd.target_name

    @classmethod
    def _get_predicate(cls, dd: DrugbankInteraction) -> str:

        return dd.target_type.name + ("" if dd.action is None else (" :: " + dd.action) + " on")


class DrugbankGeneralFunctionSearch(_DrugbankInteractionSearch[_DrugbankInteractionHit]):

    """"""

    @property
    def data_source(self) -> str:

        return "DrugBank :: non-target interactions"

    @classmethod
    def _get_obj(cls, dd: DrugbankInteraction) -> str:

        return dd.target_name if dd.general_function is None else dd.general_function

    @classmethod
    def _get_predicate(cls, dd: DrugbankInteraction) -> str:

        return ("action" if dd.action is None else dd.action) + " on"


__all__ = [
    "DrugbankTargetHit",
    "DrugbankGeneralFunctionHit",
    "DrugbankTargetSearch",
    "DrugbankGeneralFunctionSearch",
]


1			from dataclasses import dataclass
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2			from typing import Sequence, TypeVar, Set
3
4			from mandos.model.pubchem_api import PubchemApi
5			from mandos.model.pubchem_support.pubchem_models import DrugbankTargetType, DrugbankInteraction
6			from mandos.search.pubchem import PubchemHit, PubchemSearch
7
8
9			@dataclass(frozen=True, order=True, repr=True)
10			class _DrugbankInteractionHit(PubchemHit):
11			""""""
12
13			gene_symbol: str
14			protein_id: str
15			target_type: str
16			target_name: str
17			general_function: str
18
19
20			@dataclass(frozen=True, order=True, repr=True)
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
21			class DrugbankTargetHit(_DrugbankInteractionHit):
22			""""""
23
24
25			@dataclass(frozen=True, order=True, repr=True)
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
26			class DrugbankGeneralFunctionHit(_DrugbankInteractionHit):
27			""""""
28
29
30			T = TypeVar("T", bound=_DrugbankInteractionHit, covariant=True)
			0 ignored issues – show Coding Style Naming introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Class name "T" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
31
32
33			class _DrugbankInteractionSearch(PubchemSearch[T]):
34			def __init__(self, key: str, api: PubchemApi, target_types: Set[DrugbankTargetType]):
35			super().__init__(key, api)
36			self.target_types = target_types
37
38			""""""
			0 ignored issues – show Unused Code introduced 2021-03-31 03:41 UTC by Report Bug Copy Issue Report This string statement has no effect and could be removed. Loading history...
39
40			@classmethod
41			def _get_obj(cls, dd: DrugbankInteraction) -> str:
			0 ignored issues – show Coding Style Naming introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Argument name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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			raise NotImplementedError()
43
44			@classmethod
45			def _get_predicate(cls, dd: DrugbankInteraction) -> str:
			0 ignored issues – show Coding Style Naming introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Argument name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
46			raise NotImplementedError()
47
48			def find(self, inchikey: str) -> Sequence[T]:
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
49			data = self.api.fetch_data(inchikey)
50			# noinspection PyPep8Naming
51			H = self.__class__.get_h()
			0 ignored issues – show Coding Style Naming introduced 2021-03-31 03:41 UTC by Report Bug Copy Issue Report Variable name "H" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
52			return [
53			H(
54			record_id=dd.record_id,
55			origin_inchikey=inchikey,
56			matched_inchikey=data.names_and_identifiers.inchikey,
57			compound_id=str(data.cid),
58			compound_name=data.name,
59			predicate=self._get_predicate(dd),
60			object_id=self._get_obj(dd),
61			object_name=self._get_obj(dd),
62			search_key=self.key,
63			search_class=self.search_class,
64			data_source=self.data_source,
65			gene_symbol=dd.gene_symbol,
66			protein_id=dd.protein_id,
67			target_type=dd.target_type.name,
68			target_name=dd.target_name,
69			general_function=dd.general_function,
70			)
71			for dd in data.biomolecular_interactions_and_pathways.drugbank_interactions
72			if dd.target_type in self.target_types
73			]
74
75
76			class DrugbankTargetSearch(_DrugbankInteractionSearch[_DrugbankInteractionHit]):
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
77			""""""
78
79			@property
80			def data_source(self) -> str:
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
81			return "DrugBank :: target interactions"
82
83			@classmethod
84			def _get_obj(cls, dd: DrugbankInteraction) -> str:
			0 ignored issues – show Coding Style Naming introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Argument name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
85			return dd.target_name
86
87			@classmethod
88			def _get_predicate(cls, dd: DrugbankInteraction) -> str:
			0 ignored issues – show Coding Style Naming introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Argument name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
89			return dd.target_type.name + ("" if dd.action is None else (" :: " + dd.action) + " on")
90
91
92			class DrugbankGeneralFunctionSearch(_DrugbankInteractionSearch[_DrugbankInteractionHit]):
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
93			""""""
94
95			@property
96			def data_source(self) -> str:
			0 ignored issues – show introduced 2021-04-04 05:57 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
97			return "DrugBank :: non-target interactions"
98
99			@classmethod
100			def _get_obj(cls, dd: DrugbankInteraction) -> str:
			0 ignored issues – show Coding Style Naming introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Argument name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
101			return dd.target_name if dd.general_function is None else dd.general_function
102
103			@classmethod
104			def _get_predicate(cls, dd: DrugbankInteraction) -> str:
			0 ignored issues – show Coding Style Naming introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Argument name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
105			return ("action" if dd.action is None else dd.action) + " on"
106
107
108			__all__ = [
109			"DrugbankTargetHit",
110			"DrugbankGeneralFunctionHit",
111			"DrugbankTargetSearch",
112			"DrugbankGeneralFunctionSearch",
113			]
114

dmyersturnbull / mandos

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DrugbankTargetSearch._get_predicate() A

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