mandos.model.apis.chembl_support.chembl_utils.ChemblUtils._get_compound() - 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

ChemblUtils._get_compound() B

↳ Parent: mandos.model.apis.chembl_support.chembl_utils

Complexity

Conditions

Size

Total Lines	14
Code Lines	12

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	6
eloc	12
nop	2
dl	0
loc	14
rs	8.6666
c	0
b	0
f	0

from __future__ import annotations


import enum
from json.decoder import JSONDecodeError


import numpy as np

from pocketutils.core.dot_dict import NestedDotDict

from pocketutils.tools.common_tools import CommonTools

from requests.exceptions import RequestException

from urllib3.exceptions import HTTPError


from mandos import logger
from mandos.model import CompoundNotFoundError
from mandos.model.utils import CleverEnum
from mandos.model.apis.chembl_api import ChemblApi
from mandos.model.apis.chembl_support import ChemblCompound


class MolStructureType(CleverEnum):

    mol = enum.auto()
    both = enum.auto()
    none = enum.auto()


class ChemblUtils:

    def __init__(self, api: ChemblApi):
        self.api = api

    def get_target(self, chembl: str) -> NestedDotDict:
        """
        Queries for the target.

        Args:
            chembl:

        Returns:

        """
        targets = self.api.target.filter(target_chembl_id=chembl)
        if len(targets) != 1:
            raise AssertionError(f"There are {len(targets)} targets: {targets}")
        return NestedDotDict(targets[0])

    def get_compound(self, inchikey: str) -> ChemblCompound:
        """
        Calls ``get_compound_dot_dict`` and then ``compound_dot_dict_to_obj``.
        """
        ch = self.get_compound_dot_dict(inchikey)

        return self.compound_dot_dict_to_obj(ch)

    def compound_dot_dict_to_obj(self, ch: NestedDotDict) -> ChemblCompound:
class Foo:
    def some_method(self, x, y):
        return x + y;
        """
        Turn results from ``get_compound_dot_dict`` into a ``ChemblCompound``.
        """
        chid = ch["molecule_chembl_id"]
        mol_type = MolStructureType.of(ch["structure_type"])
        if mol_type == MolStructureType.none:
            logger.info(f"No structure found for compound {chid} of type {mol_type.name}.")
            logger.debug(f"No structure found for compound {ch}.")
            inchikey = "N/A"
            inchi = "N/A"
        else:
            inchi = ch["molecule_structures"]["standard_inchi"]
            inchikey = ch["molecule_structures"]["standard_inchi_key"]
        name = ch["pref_name"]
        return ChemblCompound(chid, inchikey, name, inchi)

    def get_compound_dot_dict(self, inchikey: str) -> NestedDotDict:
        """
        Fetches info and put into a dict.

        Args:
            inchikey:

        Returns:
            **Only** ``molecule_chembl_id``, ``pref_name``, "and ``molecule_structures`` are guaranteed to exist

        """
        ch = self._get_compound(inchikey)

        # molecule_hierarchy can have the actual value None
        if ch.get("molecule_hierarchy") is not None:
            parent = ch["molecule_hierarchy"]["parent_chembl_id"]
            if parent != ch["molecule_chembl_id"]:
                ch = NestedDotDict(self._get_compound(parent))

        else:
            logger.caution(f"Missing hierarchy for {ch}")
        return ch

    def _get_compound_from_smiles(self, smiles: str) -> NestedDotDict:
        try:
            results = list(
                self.api.molecule.filter(
                    molecule_structures__canonical_smiles__flexmatch=smiles
                ).only(["molecule_chembl_id", "pref_name", "molecule_structures"])
            )
        except (HTTPError, RequestException):
            raise CompoundNotFoundError(f"NOT FOUND: ChEMBL compound {smiles}")
        if len(results) != 1:
            raise CompoundNotFoundError(f"Got {len(results)} for compound {smiles}")
        result = results[0]
        if result is None:
            raise CompoundNotFoundError(f"Result for compound {smiles} is null!")
        return NestedDotDict(result)

    def _get_compound(self, inchikey: str) -> NestedDotDict:
        # saves a slow query
        if CommonTools.is_null(inchikey) or str(inchikey) == "nan":
            raise TypeError(f"Cannot get ChEMBL compound from {inchikey} (type {type(inchikey)}")
        # noinspection PyBroadException
        try:
            result = self.api.molecule.get(inchikey)
            if result is None:
                raise CompoundNotFoundError(f"Result for compound {inchikey} is null!")
            return NestedDotDict(result)
        except (HTTPError, RequestException):
            raise CompoundNotFoundError(f"Failed to find compound {inchikey}")
        except Exception:

            logger.error(f"Error on ChEMBL query for compound {inchikey}")


__all__ = ["MolStructureType", "ChemblUtils"]


1			from __future__ import annotations
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2
3			import enum
4			from json.decoder import JSONDecodeError
			0 ignored issues – show Unused Code introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unused JSONDecodeError imported from json.decoder Loading history...
5
6			import numpy as np
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unable to import 'numpy' Loading history... Unused Code introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unused numpy imported as np Loading history...
7			from pocketutils.core.dot_dict import NestedDotDict
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.dot_dict' Loading history...
8			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...
9			from requests.exceptions import RequestException
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'requests.exceptions' Loading history...
10			from urllib3.exceptions import HTTPError
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'urllib3.exceptions' Loading history...
11
12			from mandos import logger
13			from mandos.model import CompoundNotFoundError
14			from mandos.model.utils import CleverEnum
15			from mandos.model.apis.chembl_api import ChemblApi
16			from mandos.model.apis.chembl_support import ChemblCompound
17
18
19			class MolStructureType(CleverEnum):
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
20			mol = enum.auto()
21			both = enum.auto()
22			none = enum.auto()
23
24
25			class ChemblUtils:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
26			def __init__(self, api: ChemblApi):
27			self.api = api
28
29			def get_target(self, chembl: str) -> NestedDotDict:
30			"""
31			Queries for the target.
32
33			Args:
34			chembl:
35
36			Returns:
37
38			"""
39			targets = self.api.target.filter(target_chembl_id=chembl)
40			if len(targets) != 1:
41			raise AssertionError(f"There are {len(targets)} targets: {targets}")
42			return NestedDotDict(targets[0])
43
44			def get_compound(self, inchikey: str) -> ChemblCompound:
45			"""
46			Calls ``get_compound_dot_dict`` and then ``compound_dot_dict_to_obj``.
47			"""
48			ch = self.get_compound_dot_dict(inchikey)
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "ch" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
49			return self.compound_dot_dict_to_obj(ch)
50
51			def compound_dot_dict_to_obj(self, ch: NestedDotDict) -> ChemblCompound:
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history... Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Argument name "ch" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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			"""
53			Turn results from ``get_compound_dot_dict`` into a ``ChemblCompound``.
54			"""
55			chid = ch["molecule_chembl_id"]
56			mol_type = MolStructureType.of(ch["structure_type"])
57			if mol_type == MolStructureType.none:
58			logger.info(f"No structure found for compound {chid} of type {mol_type.name}.")
59			logger.debug(f"No structure found for compound {ch}.")
60			inchikey = "N/A"
61			inchi = "N/A"
62			else:
63			inchi = ch["molecule_structures"]["standard_inchi"]
64			inchikey = ch["molecule_structures"]["standard_inchi_key"]
65			name = ch["pref_name"]
66			return ChemblCompound(chid, inchikey, name, inchi)
67
68			def get_compound_dot_dict(self, inchikey: str) -> NestedDotDict:
69			"""
70			Fetches info and put into a dict.
71
72			Args:
73			inchikey:
74
75			Returns:
76			Only ``molecule_chembl_id``, ``pref_name``, "and ``molecule_structures`` are guaranteed to exist
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (112/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
77			"""
78			ch = self._get_compound(inchikey)
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "ch" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
79			# molecule_hierarchy can have the actual value None
80			if ch.get("molecule_hierarchy") is not None:
81			parent = ch["molecule_hierarchy"]["parent_chembl_id"]
82			if parent != ch["molecule_chembl_id"]:
83			ch = NestedDotDict(self._get_compound(parent))
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "ch" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
84			else:
85			logger.caution(f"Missing hierarchy for {ch}")
86			return ch
87
88			def _get_compound_from_smiles(self, smiles: str) -> NestedDotDict:
89			try:
90			results = list(
91			self.api.molecule.filter(
92			molecule_structures__canonical_smiles__flexmatch=smiles
93			).only(["molecule_chembl_id", "pref_name", "molecule_structures"])
94			)
95			except (HTTPError, RequestException):
96			raise CompoundNotFoundError(f"NOT FOUND: ChEMBL compound {smiles}")
97			if len(results) != 1:
98			raise CompoundNotFoundError(f"Got {len(results)} for compound {smiles}")
99			result = results[0]
100			if result is None:
101			raise CompoundNotFoundError(f"Result for compound {smiles} is null!")
102			return NestedDotDict(result)
103
104			def _get_compound(self, inchikey: str) -> NestedDotDict:
105			# saves a slow query
106			if CommonTools.is_null(inchikey) or str(inchikey) == "nan":
107			raise TypeError(f"Cannot get ChEMBL compound from {inchikey} (type {type(inchikey)}")
108			# noinspection PyBroadException
109			try:
110			result = self.api.molecule.get(inchikey)
111			if result is None:
112			raise CompoundNotFoundError(f"Result for compound {inchikey} is null!")
113			return NestedDotDict(result)
114			except (HTTPError, RequestException):
115			raise CompoundNotFoundError(f"Failed to find compound {inchikey}")
116			except Exception:
			0 ignored issues – show Best Practice introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Catching very general exceptions such as `Exception` is usually not recommended. Generally, you would want to handle very specific errors in the exception handler. This ensure that you do not hide other types of errors which should be fixed. So, unless you specifically plan to handle any error, consider adding a more specific exception. Loading history...
117			logger.error(f"Error on ChEMBL query for compound {inchikey}")
118
119
120			__all__ = ["MolStructureType", "ChemblUtils"]
121

dmyersturnbull / mandos

Push — main ( 9813db...5006f2 )

ChemblUtils._get_compound() B

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