mandos.search.pubchem.drugbank_interaction_search._DrugbankInteractionSearch.find() - Code Metrics - Inspection of "fix: misc" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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by Douglas

created 2021-11-04 01:01 UTC

_DrugbankInteractionSearch.find() B

↳ Parent: mandos.search.pubchem.drugbank_interaction_search

Complexity

Conditions

Size

Total Lines	31
Code Lines	28

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	5
eloc	28
nop	2
dl	0
loc	31
rs	8.7413
c	0
b	0
f	0

from typing import Optional, Sequence, Set, TypeVar


from mandos.model.apis.pubchem_api import PubchemApi
from mandos.model.apis.pubchem_support.pubchem_models import (
    DrugbankInteraction,
    DrugbankTargetType,
)

# noinspection PyProtectedMember
from mandos.model.concrete_hits import (
    DrugbankGeneralFunctionHit,
    DrugbankTargetHit,
    _DrugbankInteractionHit,
)
from mandos.search.pubchem import PubchemSearch

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



# noinspection PyAbstractClass
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) -> Optional[str]:

        raise NotImplementedError()

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

        data = self.api.fetch_data(inchikey)
        results = []
        for dd in data.biomolecular_interactions_and_pathways.drugbank_interactions:

            if dd.target_type in self.target_types:
                source = self._format_source(type=dd.target_type.name)
                predicate = self._format_predicate(
                    type=dd.target_type.name,
                    action="generic" if dd.action is None else dd.action,
                )
                obj = self._get_obj(dd)
                if obj is not None:
                    results.append(
                        self._create_hit(
                            c_id=str(data.cid),
                            c_origin=inchikey,
                            c_matched=data.names_and_identifiers.inchikey,
                            c_name=data.name,
                            data_source=source,
                            predicate=predicate,
                            object_id=obj,
                            object_name=obj,
                            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,
                            cache_date=data.names_and_identifiers.modify_date,
                        )
                    )
        return results


class DrugbankTargetSearch(_DrugbankInteractionSearch[DrugbankTargetHit]):

    """ """

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

        return dd.target_name


class DrugbankGeneralFunctionSearch(_DrugbankInteractionSearch[DrugbankGeneralFunctionHit]):

    """ """

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

        return dd.general_function  # might be None


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


1			from typing import Optional, Sequence, Set, TypeVar
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2
3			from mandos.model.apis.pubchem_api import PubchemApi
4			from mandos.model.apis.pubchem_support.pubchem_models import (
5			DrugbankInteraction,
6			DrugbankTargetType,
7			)
8
9			# noinspection PyProtectedMember
10			from mandos.model.concrete_hits import (
11			DrugbankGeneralFunctionHit,
12			DrugbankTargetHit,
13			_DrugbankInteractionHit,
14			)
15			from mandos.search.pubchem import PubchemSearch
16
17			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_]+$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
18
19
20			# noinspection PyAbstractClass
21			class _DrugbankInteractionSearch(PubchemSearch[T]):
22			def __init__(self, key: str, api: PubchemApi, target_types: Set[DrugbankTargetType]):
23			super().__init__(key, api)
24			self.target_types = target_types
25
26			@classmethod
27			def _get_obj(cls, dd: DrugbankInteraction) -> Optional[str]:
			0 ignored issues – show Coding Style Naming introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Argument name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
28			raise NotImplementedError()
29
30			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...
31			data = self.api.fetch_data(inchikey)
32			results = []
33			for dd in data.biomolecular_interactions_and_pathways.drugbank_interactions:
			0 ignored issues – show Coding Style Naming introduced 2021-11-04 01:02 UTC by Report Bug Copy Issue Report Variable name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
34			if dd.target_type in self.target_types:
35			source = self._format_source(type=dd.target_type.name)
36			predicate = self._format_predicate(
37			type=dd.target_type.name,
38			action="generic" if dd.action is None else dd.action,
39			)
40			obj = self._get_obj(dd)
41			if obj is not None:
42			results.append(
43			self._create_hit(
44			c_id=str(data.cid),
45			c_origin=inchikey,
46			c_matched=data.names_and_identifiers.inchikey,
47			c_name=data.name,
48			data_source=source,
49			predicate=predicate,
50			object_id=obj,
51			object_name=obj,
52			gene_symbol=dd.gene_symbol,
53			protein_id=dd.protein_id,
54			target_type=dd.target_type.name,
55			target_name=dd.target_name,
56			general_function=dd.general_function,
57			cache_date=data.names_and_identifiers.modify_date,
58			)
59			)
60			return results
61
62
63			class DrugbankTargetSearch(_DrugbankInteractionSearch[DrugbankTargetHit]):
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
64			""" """
65
66			@classmethod
67			def _get_obj(cls, dd: DrugbankInteraction) -> Optional[str]:
			0 ignored issues – show Coding Style Naming introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Argument name "dd" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
68			return dd.target_name
69
70
71			class DrugbankGeneralFunctionSearch(_DrugbankInteractionSearch[DrugbankGeneralFunctionHit]):
			0 ignored issues – show Documentation introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
72			""" """
73
74			@classmethod
75			def _get_obj(cls, dd: DrugbankInteraction) -> Optional[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...
76			return dd.general_function # might be None
77
78
79			__all__ = [
80			"DrugbankTargetSearch",
81			"DrugbankGeneralFunctionSearch",
82			]
83

dmyersturnbull / mandos

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_DrugbankInteractionSearch.find() B

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