mandos.model.apis.hmdb_api.JsonBackedHmdbApi._prop() - Code Metrics - Inspection of "feat: add prediction search; improve taxa" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( 9813db...5006f2 )

by Douglas

created 2021-08-07 00:13 UTC

JsonBackedHmdbApi._prop() B

↳ Parent: mandos.model.apis.hmdb_api

Complexity

Conditions

Size

Total Lines	14
Code Lines	14

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	6
eloc	14
nop	3
dl	0
loc	14
rs	8.6666
c	0
b	0
f	0

import abc

import gzip
from pathlib import Path
from dataclasses import dataclass
from typing import Union, Sequence, Optional

import defusedxml.ElementTree as Xml

import orjson

from pocketutils.tools.common_tools import CommonTools


from mandos.model.settings import QUERY_EXECUTORS, MANDOS_SETTINGS
from pocketutils.core.dot_dict import NestedDotDict

from pocketutils.core.query_utils import QueryExecutor


from mandos.model import Api



def _is_float(s):

    try:
        float(s)
        return True
    except ValueError:
        return False


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

class HmdbProperty:
    name: str
    source: str
    value: Union[None, str, int, float, bool]
    experimental: bool


class HmdbApi(Api, metaclass=abc.ABCMeta):

    def fetch(self, hmdb_id: str) -> NestedDotDict:

        raise NotImplementedError()

    def fetch_properties(self, hmdb_id: str) -> Sequence[HmdbProperty]:

        raise NotImplementedError()

    def fetch_tissues(self, hmdb_id: str) -> Sequence[HmdbProperty]:

        raise NotImplementedError()


class JsonBackedHmdbApi(HmdbApi, metaclass=abc.ABCMeta):

    def fetch_properties(self, hmdb_id: str) -> Sequence[HmdbProperty]:
        data = self.fetch(hmdb_id)
        pred = data.sub("metabolite.predicted_properties.property")
        exp = data.sub("metabolite.experimental_properties.property")
        items = [self._prop(x, True) for x in exp]
        items += [self._prop(x, False) for x in pred]
        return items

    def fetch_tissues(self, hmdb_id: str) -> Sequence[str]:
        data = self.fetch(hmdb_id)
        tissues = data.get_list_as("metabolite.biological_properties.tissue_locations.tissue", str)
        return [] if tissues is None else tissues

    def _prop(self, x: NestedDotDict, experimental: bool):
class Foo:
    def some_method(self, x, y):
        return x + y;
        value = x.req_as("value", str)
        if value.isdigit():
            value = int(value)
        elif value.lower() == "true":
            value = True
        elif value.lower() == "false":
            value = False
        elif CommonTools.is_probable_null(value):
            value = None
        elif _is_float(value):
            value = float(value)
        return HmdbProperty(
            name=x["kind"], value=value, source=x["source"], experimental=experimental
        )


class QueryingHmdbApi(JsonBackedHmdbApi):

    def __init__(self, executor: QueryExecutor = QUERY_EXECUTORS.hmdb):
        self._executor = executor

    def fetch(self, hmdb_id: str) -> NestedDotDict:
        # e.g. https://hmdb.ca/metabolites/HMDB0001925.xml
        url = f"https://hmdb.ca/metabolites/{hmdb_id}.xml"
        data = self._executor(url)
        data = self._to_json(data)
        return NestedDotDict(data)

    def _to_json(self, xml):
        response = {}
        for child in list(xml):
            if len(list(child)) > 0:
                response[child.tag] = self._to_json(child)
            else:
                response[child.tag] = child.text or ""
        return response


class CachingHmdbApi(JsonBackedHmdbApi):

    def __init__(
        self, query: Optional[QueryingHmdbApi], cache_dir: Path = MANDOS_SETTINGS.hmdb_cache_path

    ):
        self._query = query
        self._cache_dir = cache_dir

    def fetch(self, hmdb_id: str) -> NestedDotDict:
        path = self.path(hmdb_id)
        if not path.exists():

            return self._read_json(path)
        else:
            data = self._query.fetch(hmdb_id)
            self._write_json(data, path)
            return data

    def path(self, hmdb_id: str):

        return (self._cache_dir / hmdb_id).with_suffix(".json.gz")

    def _write_json(self, data: NestedDotDict, path: Path) -> None:
class Foo:
    def some_method(self, x, y):
        return x + y;
        path.write_bytes(gzip.compress(data.to_json()))

    def _read_json(self, path: Path) -> NestedDotDict:
class Foo:
    def some_method(self, x, y):
        return x + y;
        deflated = gzip.decompress(path.read_bytes())
        read = orjson.loads(deflated)
        return NestedDotDict(read)


__all__ = ["HmdbApi", "QueryingHmdbApi", "HmdbProperty"]


1			import abc
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2			import gzip
3			from pathlib import Path
4			from dataclasses import dataclass
5			from typing import Union, Sequence, Optional
6
7			import defusedxml.ElementTree as Xml
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Unable to import 'defusedxml.ElementTree' Loading history... Unused Code introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Unused defusedxml.ElementTree imported as Xml Loading history...
8			import orjson
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unable to import 'orjson' Loading history...
9			from pocketutils.tools.common_tools import CommonTools
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.tools.common_tools' Loading history...
10
11			from mandos.model.settings import QUERY_EXECUTORS, MANDOS_SETTINGS
12			from pocketutils.core.dot_dict import NestedDotDict
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.dot_dict' Loading history... introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Imports from package pocketutils are not grouped Loading history...
13			from pocketutils.core.query_utils import QueryExecutor
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.query_utils' Loading history...
14
15			from mandos.model import Api
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Imports from package mandos are not grouped Loading history...
16
17
18			def _is_float(s):
			0 ignored issues – show Coding Style Naming introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Argument 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...
19			try:
20			float(s)
21			return True
22			except ValueError:
23			return False
24
25
26			@dataclass(frozen=True, repr=True, order=True)
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
27			class HmdbProperty:
28			name: str
29			source: str
30			value: Union[None, str, int, float, bool]
31			experimental: bool
32
33
34			class HmdbApi(Api, metaclass=abc.ABCMeta):
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
35			def fetch(self, hmdb_id: str) -> NestedDotDict:
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
36			raise NotImplementedError()
37
38			def fetch_properties(self, hmdb_id: str) -> Sequence[HmdbProperty]:
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
39			raise NotImplementedError()
40
41			def fetch_tissues(self, hmdb_id: str) -> Sequence[HmdbProperty]:
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
42			raise NotImplementedError()
43
44
45			class JsonBackedHmdbApi(HmdbApi, metaclass=abc.ABCMeta):
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
46			def fetch_properties(self, hmdb_id: str) -> Sequence[HmdbProperty]:
47			data = self.fetch(hmdb_id)
48			pred = data.sub("metabolite.predicted_properties.property")
49			exp = data.sub("metabolite.experimental_properties.property")
50			items = [self._prop(x, True) for x in exp]
51			items += [self._prop(x, False) for x in pred]
52			return items
53
54			def fetch_tissues(self, hmdb_id: str) -> Sequence[str]:
55			data = self.fetch(hmdb_id)
56			tissues = data.get_list_as("metabolite.biological_properties.tissue_locations.tissue", str)
57			return [] if tissues is None else tissues
58
59			def _prop(self, x: NestedDotDict, experimental: bool):
			0 ignored issues – show Coding Style Naming introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Argument 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... Coding Style introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
60			value = x.req_as("value", str)
61			if value.isdigit():
62			value = int(value)
63			elif value.lower() == "true":
64			value = True
65			elif value.lower() == "false":
66			value = False
67			elif CommonTools.is_probable_null(value):
68			value = None
69			elif _is_float(value):
70			value = float(value)
71			return HmdbProperty(
72			name=x["kind"], value=value, source=x["source"], experimental=experimental
73			)
74
75
76			class QueryingHmdbApi(JsonBackedHmdbApi):
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
77			def __init__(self, executor: QueryExecutor = QUERY_EXECUTORS.hmdb):
78			self._executor = executor
79
80			def fetch(self, hmdb_id: str) -> NestedDotDict:
81			# e.g. https://hmdb.ca/metabolites/HMDB0001925.xml
82			url = f"https://hmdb.ca/metabolites/{hmdb_id}.xml"
83			data = self._executor(url)
84			data = self._to_json(data)
85			return NestedDotDict(data)
86
87			def _to_json(self, xml):
88			response = {}
89			for child in list(xml):
90			if len(list(child)) > 0:
91			response[child.tag] = self._to_json(child)
92			else:
93			response[child.tag] = child.text or ""
94			return response
95
96
97			class CachingHmdbApi(JsonBackedHmdbApi):
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
98			def __init__(
99			self, query: Optional[QueryingHmdbApi], cache_dir: Path = MANDOS_SETTINGS.hmdb_cache_path
			0 ignored issues – show Coding Style introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
100			):
101			self._query = query
102			self._cache_dir = cache_dir
103
104			def fetch(self, hmdb_id: str) -> NestedDotDict:
105			path = self.path(hmdb_id)
106			if not path.exists():
			0 ignored issues – show unused-code introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history...
107			return self._read_json(path)
108			else:
109			data = self._query.fetch(hmdb_id)
110			self._write_json(data, path)
111			return data
112
113			def path(self, hmdb_id: str):
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
114			return (self._cache_dir / hmdb_id).with_suffix(".json.gz")
115
116			def _write_json(self, data: NestedDotDict, path: Path) -> None:
			0 ignored issues – show Coding Style introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
117			path.write_bytes(gzip.compress(data.to_json()))
118
119			def _read_json(self, path: Path) -> NestedDotDict:
			0 ignored issues – show Coding Style introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
120			deflated = gzip.decompress(path.read_bytes())
121			read = orjson.loads(deflated)
122			return NestedDotDict(read)
123
124
125			__all__ = ["HmdbApi", "QueryingHmdbApi", "HmdbProperty"]
126

dmyersturnbull / mandos

Push — main ( 9813db...5006f2 )

JsonBackedHmdbApi._prop() B

Complexity

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Duplication

Importance

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