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

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Push — main ( 2e1b6b...3a0c28 )

by Douglas

created 2021-11-04 01:01 UTC

AcuteEffectSearch.find() B

↳ Parent: mandos.search.pubchem.acute_effects_search

Complexity

Conditions

Size

Total Lines	46
Code Lines	41

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	5
eloc	41
nop	2
dl	0
loc	46
rs	8.4293
c	0
b	0
f	0

from typing import Sequence


import numpy as np


from mandos.model.apis.pubchem_api import PubchemApi
from mandos.model.concrete_hits import AcuteEffectHit, Ld50Hit
from mandos.model.utils.setup import logger
from mandos.search.pubchem import PubchemSearch


class AcuteEffectSearch(PubchemSearch[AcuteEffectHit]):

    """ """

    def __init__(self, key: str, api: PubchemApi, top_level: bool):
        super().__init__(key, api)
        self.top_level = top_level

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

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

            for effect in dd.effects:
                effect_name = effect.category.lower() if self.top_level else effect.lower()
                try:
                    weight = -dd.mg_per_kg
                except ValueError:
                    logger.error(f"Failed to parse {dd.dose} on {inchikey}")
                    logger.opt(exception=True).debug(
                        f"Failed to parse {dd.dose} on {inchikey}: {dd}"
                    )
                    continue
                source = self._format_source(
                    organism=dd.organism,
                    human=dd.organism.is_human,
                    route=dd.route,
                    test_type=dd.test_type,
                )
                predicate = self._format_predicate(
                    organism=dd.organism,
                    human=dd.organism.is_human,
                    route=dd.route,
                    test_type=dd.test_type,
                )
                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=effect_name,
                        object_name=effect_name,
                        effect=effect.lower(),
                        organism=dd.organism,
                        human=dd.organism.is_human,
                        route=dd.route,
                        mg_per_kg=dd.mg_per_kg,
                        test_type=dd.test_type,
                        weight=weight,
                    )
                )
        return results


class Ld50Search(PubchemSearch[Ld50Hit]):

    def find(self, inchikey: str) -> Sequence[Ld50Hit]:

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

            if dd.test_type != "LD50":
                continue
            try:
                weight = -dd.mg_per_kg
            except ValueError:
                logger.error(f"Failed to parse {dd.dose} on {inchikey}")
                logger.opt(exception=True).debug(f"Failed to parse {dd.dose} on {inchikey}: {dd}")
                continue
            logger.trace(f"NLP: Weight {weight} from {dd.mg_per_kg}")
            source = self._format_source(
                organism=dd.organism,
                human=dd.organism.is_human,
                route=dd.route,
                test_type=dd.test_type,
            )
            predicate = self._format_predicate(
                organism=dd.organism,
                human=dd.organism.is_human,
                route=dd.route,
                test_type=dd.test_type,
            )
            results.append(
                self._create_hit(
                    inchikey=inchikey,
                    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=str(dd.mg_per_kg),
                    object_name=str(dd.mg_per_kg),
                    weight=weight,
                    organism=dd.organism,
                    human=dd.organism.is_human,
                    route=dd.route,
                    cache_date=data.names_and_identifiers.modify_date,
                )
            )
        return results


__all__ = ["AcuteEffectSearch", "Ld50Search"]


1			from typing import Sequence
			0 ignored issues – show introduced 2021-03-31 03:41 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2
3			import numpy as np
			0 ignored issues – show introduced 2021-08-16 03:00 UTC by Report Bug Copy Issue Report Unable to import 'numpy' Loading history... Unused Code introduced 2021-11-04 01:02 UTC by Report Bug Copy Issue Report Unused numpy imported as np Loading history...
4
5			from mandos.model.apis.pubchem_api import PubchemApi
6			from mandos.model.concrete_hits import AcuteEffectHit, Ld50Hit
7			from mandos.model.utils.setup import logger
8			from mandos.search.pubchem import PubchemSearch
9
10
11			class AcuteEffectSearch(PubchemSearch[AcuteEffectHit]):
			0 ignored issues – show Documentation introduced 2021-03-31 03:41 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
12			""" """
13
14			def __init__(self, key: str, api: PubchemApi, top_level: bool):
15			super().__init__(key, api)
16			self.top_level = top_level
17
18			def find(self, inchikey: str) -> Sequence[AcuteEffectHit]:
			0 ignored issues – show introduced 2021-03-31 03:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
19			data = self.api.fetch_data(inchikey)
20			results = []
21			for dd in data.toxicity.acute_effects:
			0 ignored issues – show Coding Style Naming introduced 2021-03-31 03:41 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...
22			for effect in dd.effects:
23			effect_name = effect.category.lower() if self.top_level else effect.lower()
24			try:
25			weight = -dd.mg_per_kg
26			except ValueError:
27			logger.error(f"Failed to parse {dd.dose} on {inchikey}")
28			logger.opt(exception=True).debug(
29			f"Failed to parse {dd.dose} on {inchikey}: {dd}"
30			)
31			continue
32			source = self._format_source(
33			organism=dd.organism,
34			human=dd.organism.is_human,
35			route=dd.route,
36			test_type=dd.test_type,
37			)
38			predicate = self._format_predicate(
39			organism=dd.organism,
40			human=dd.organism.is_human,
41			route=dd.route,
42			test_type=dd.test_type,
43			)
44			results.append(
45			self._create_hit(
46			c_id=str(data.cid),
47			c_origin=inchikey,
48			c_matched=data.names_and_identifiers.inchikey,
49			c_name=data.name,
50			data_source=source,
51			predicate=predicate,
52			object_id=effect_name,
53			object_name=effect_name,
54			effect=effect.lower(),
55			organism=dd.organism,
56			human=dd.organism.is_human,
57			route=dd.route,
58			mg_per_kg=dd.mg_per_kg,
59			test_type=dd.test_type,
60			weight=weight,
61			)
62			)
63			return results
64
65
66			class Ld50Search(PubchemSearch[Ld50Hit]):
			0 ignored issues – show introduced 2021-03-31 03:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
67			def find(self, inchikey: str) -> Sequence[Ld50Hit]:
			0 ignored issues – show introduced 2021-03-31 03:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
68			data = self.api.fetch_data(inchikey)
69			results = []
70			for dd in data.toxicity.acute_effects:
			0 ignored issues – show Coding Style Naming introduced 2021-03-31 03:41 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...
71			if dd.test_type != "LD50":
72			continue
73			try:
74			weight = -dd.mg_per_kg
75			except ValueError:
76			logger.error(f"Failed to parse {dd.dose} on {inchikey}")
77			logger.opt(exception=True).debug(f"Failed to parse {dd.dose} on {inchikey}: {dd}")
78			continue
79			logger.trace(f"NLP: Weight {weight} from {dd.mg_per_kg}")
80			source = self._format_source(
81			organism=dd.organism,
82			human=dd.organism.is_human,
83			route=dd.route,
84			test_type=dd.test_type,
85			)
86			predicate = self._format_predicate(
87			organism=dd.organism,
88			human=dd.organism.is_human,
89			route=dd.route,
90			test_type=dd.test_type,
91			)
92			results.append(
93			self._create_hit(
94			inchikey=inchikey,
95			c_id=str(data.cid),
96			c_origin=inchikey,
97			c_matched=data.names_and_identifiers.inchikey,
98			c_name=data.name,
99			data_source=source,
100			predicate=predicate,
101			object_id=str(dd.mg_per_kg),
102			object_name=str(dd.mg_per_kg),
103			weight=weight,
104			organism=dd.organism,
105			human=dd.organism.is_human,
106			route=dd.route,
107			cache_date=data.names_and_identifiers.modify_date,
108			)
109			)
110			return results
111
112
113			__all__ = ["AcuteEffectSearch", "Ld50Search"]
114

dmyersturnbull / mandos

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AcuteEffectSearch.find() B

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