mandos.model.apis.hmdb_api

Complexity

Total Complexity

20

Size/Duplication

Total Lines	108
Duplicated Lines	0 %

Importance

Changes

0

11 Methods

Rating	Name	Duplication	Size	Complexity
A	QueryingHmdbApi.__init__()	0	2	1
A	CachingHmdbApi.fetch()	0	9	2
A	JsonBackedHmdbApi.fetch_tissues()	0	4	2
A	CachingHmdbApi.__init__()	0	5	1
A	HmdbApi.fetch()	0	2	1
A	HmdbApi.fetch_properties()	0	2	1
A	HmdbApi.fetch_tissues()	0	2	1
B	JsonBackedHmdbApi._prop()	0	14	6
A	JsonBackedHmdbApi.fetch_properties()	0	7	1
A	QueryingHmdbApi._to_json()	0	8	3
A	QueryingHmdbApi.fetch()	0	6	1

import abc

Missing module docstring

import gzip

The import gzip seems to be unused.

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

import decorateme

Unable to import 'decorateme'

import orjson

Unable to import 'orjson'

The import orjson seems to be unused.

from pocketutils.core.dot_dict import NestedDotDict

Unable to import 'pocketutils.core.dot_dict'

from pocketutils.core.query_utils import QueryExecutor

Unable to import 'pocketutils.core.query_utils'

from pocketutils.tools.common_tools import CommonTools

Unable to import 'pocketutils.tools.common_tools'

from mandos.model import Api
from mandos.model.settings import QUERY_EXECUTORS, SETTINGS


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

Missing class docstring

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


@decorateme.auto_repr_str()

Missing class docstring

class HmdbApi(Api, metaclass=abc.ABCMeta):
    def fetch(self, hmdb_id: str) -> NestedDotDict:

Missing function or method docstring

        raise NotImplementedError()

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

Missing function or method docstring

        raise NotImplementedError()

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

Missing function or method docstring

        raise NotImplementedError()


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

Missing class docstring

    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):

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 method could be written as a function/class method.

        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 CommonTools.is_float(value):
            value = float(value)
        return HmdbProperty(
            name=x["kind"], value=value, source=x["source"], experimental=experimental
        )


class QueryingHmdbApi(JsonBackedHmdbApi):

Missing class docstring

    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):

Missing class docstring

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

Wrong hanging indentation before block (add 4 spaces).

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

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

The Instance of CachingHmdbApi does not seem to have a member named path.

        if not path.exists():

Unnecessary "else" after "return"

            return NestedDotDict.read_json(path)
        else:
            data = self._query.fetch(hmdb_id)
            data.write_json(path, mkdirs=True)
            self._write_json(data, path)

The Instance of CachingHmdbApi does not seem to have a member named _write_json.

            return data


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