mandos.entry._entry_utils.EntryUtils.adjust_filename() - Code Metrics - Inspection of "fix: small" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — main ( 9cce85...686e96 )

by Douglas

created 2021-09-13 00:13 UTC

EntryUtils.adjust_filename() C

↳ Parent: mandos.entry._entry_utils

Complexity

Conditions

Size

Total Lines	17
Code Lines	16

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	9
eloc	16
nop	4
dl	0
loc	17
rs	6.6666
c	0
b	0
f	0

from pathlib import Path

from typing import Set, Sequence, Optional, Union

from mandos.model.utils.setup import logger
from mandos.model.settings import MANDOS_SETTINGS
from mandos.model.apis.chembl_support.chembl_activity import DataValidityComment
from mandos.model.apis.chembl_support.chembl_targets import TargetType
from mandos.model.apis.pubchem_support.pubchem_models import ClinicalTrialsGovUtils
from mandos.model.taxonomy import Taxonomy
from mandos.model.taxonomy_caches import TaxonomyFactories


class EntryUtils:

    """ """

    @classmethod
    def adjust_filename(cls, to: Optional[Path], default: Union[str, Path], replace: bool) -> Path:

        if to is None:
            path = Path(default)
        elif str(to).startswith("."):
            path = Path(default).with_suffix(str(to))
        elif str(to).startswith("*."):
            path = Path(default).with_suffix(str(to)[1:])
        elif to.is_dir() or to.suffix == "":
            path = to / default
        else:
            path = Path(to)
        if path.exists() and not replace:

            raise FileExistsError(f"File {path} already exists")
        elif replace:
            logger.info(f"Overwriting existing file {path}.")
        return path

    @staticmethod
    def split(st: str) -> Set[str]:

        return {s.strip() for s in st.split(",")}

    @staticmethod
    def get_taxa(taxa: str) -> Sequence[Taxonomy]:

        factory = TaxonomyFactories.from_uniprot(MANDOS_SETTINGS.taxonomy_cache_path)
        return [factory.load(str(taxon).strip()) for taxon in taxa.split(",")]

    @staticmethod
    def get_trial_statuses(st: str) -> Set[str]:

        return ClinicalTrialsGovUtils.resolve_statuses(st)

    @staticmethod
    def get_target_types(st: str) -> Set[str]:

        return {s.name for s in TargetType.resolve(st)}

    @staticmethod
    def get_flags(st: str) -> Set[str]:

        return {s.name for s in DataValidityComment.resolve(st)}


__all__ = ["EntryUtils"]


1			from pathlib import Path
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2			from typing import Set, Sequence, Optional, Union
3
4			from mandos.model.utils.setup import logger
5			from mandos.model.settings import MANDOS_SETTINGS
6			from mandos.model.apis.chembl_support.chembl_activity import DataValidityComment
7			from mandos.model.apis.chembl_support.chembl_targets import TargetType
8			from mandos.model.apis.pubchem_support.pubchem_models import ClinicalTrialsGovUtils
9			from mandos.model.taxonomy import Taxonomy
10			from mandos.model.taxonomy_caches import TaxonomyFactories
11
12
13			class EntryUtils:
			0 ignored issues – show Documentation introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
14			""" """
15
16			@classmethod
17			def adjust_filename(cls, to: Optional[Path], default: Union[str, Path], replace: bool) -> Path:
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
18			if to is None:
19			path = Path(default)
20			elif str(to).startswith("."):
21			path = Path(default).with_suffix(str(to))
22			elif str(to).startswith("*."):
23			path = Path(default).with_suffix(str(to)[1:])
24			elif to.is_dir() or to.suffix == "":
25			path = to / default
26			else:
27			path = Path(to)
28			if path.exists() and not replace:
			0 ignored issues – show Unused Code introduced 2021-08-03 04:51 UTC by Report Bug Copy Issue Report Unnecessary "elif" after "raise" Loading history...
29			raise FileExistsError(f"File {path} already exists")
30			elif replace:
31			logger.info(f"Overwriting existing file {path}.")
32			return path
33
34			@staticmethod
35			def split(st: str) -> Set[str]:
			0 ignored issues – show Coding Style Naming introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Argument name "st" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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... introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
36			return {s.strip() for s in st.split(",")}
37
38			@staticmethod
39			def get_taxa(taxa: str) -> Sequence[Taxonomy]:
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
40			factory = TaxonomyFactories.from_uniprot(MANDOS_SETTINGS.taxonomy_cache_path)
41			return [factory.load(str(taxon).strip()) for taxon in taxa.split(",")]
42
43			@staticmethod
44			def get_trial_statuses(st: str) -> Set[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... Coding Style Naming introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Argument name "st" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
45			return ClinicalTrialsGovUtils.resolve_statuses(st)
46
47			@staticmethod
48			def get_target_types(st: str) -> Set[str]:
			0 ignored issues – show Coding Style Naming introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Argument name "st" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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... introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
49			return {s.name for s in TargetType.resolve(st)}
50
51			@staticmethod
52			def get_flags(st: str) -> Set[str]:
			0 ignored issues – show Coding Style Naming introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Argument name "st" 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... introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
53			return {s.name for s in DataValidityComment.resolve(st)}
54
55
56			__all__ = ["EntryUtils"]
57

dmyersturnbull / mandos

Push — main ( 9cce85...686e96 )

EntryUtils.adjust_filename() C

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like