tests.search.chembl.test_indication_search.TestIndicationSearch.test_find() - Code Metrics - Inspection of "feat: major refactoring" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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by Douglas

created 2021-03-10 02:36 UTC

TestIndicationSearch.test_find() A

↳ Parent: tests.search.chembl.test_indication_search

Complexity

Conditions

Size

Total Lines	22
Code Lines	20

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	20
nop	1
dl	0
loc	22
rs	9.4
c	0
b	0
f	0

import pytest


from mandos.cli import Commands, Searcher
from mandos.model.chembl_api import ChemblApi
from chembl_webresource_client.new_client import new_client as Chembl

from mandos.search.chembl.indication_search import IndicationSearch


from .. import get_test_resource


class TestIndicationSearch:

    def test_find(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        df, triples = Commands.trials(get_test_resource("inchis.txt"))

        assert len(df) == 6
        assert len(triples) == 6
        assert {t.compound_name.lower() for t in triples} == {"alprazolam"}
        assert {t.object_id for t in triples} == {
            "D012559",
            "D016584",
            "D003704",
            "D001008",
            "D001007",
            "D003866",
        }
        assert {t.object_name.lower() for t in triples} == {
            "schizophrenia",
            "panic disorder",
            "dementia",
            "anxiety",
            "depressive disorder",
            "anxiety disorders",
        }
        assert {t.predicate for t in triples} == {"phase-4 indication", "phase-3 indication"}

    def test_cocaine_hcl(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        api = ChemblApi.wrap(Chembl)
        df, triples = Searcher(IndicationSearch(api, min_phase=3)).search_for(["CHEMBL529437"])

        assert len(df) == 1
        assert len(triples) == 1
        assert triples[0].compound_name.lower() == "cocaine"
        assert triples[0].compound_id == "CHEMBL370805"
        assert triples[0].object_id == "D000758"
        assert triples[0].object_name == "Anesthesia"
        assert triples[0].predicate == "phase-4 indication"


if __name__ == "__main__":
    pytest.main()


1			import pytest
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'pytest' Loading history... introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2
3			from mandos.cli import Commands, Searcher
4			from mandos.model.chembl_api import ChemblApi
5			from chembl_webresource_client.new_client import new_client as Chembl
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Unable to import 'chembl_webresource_client.new_client' Loading history...
6			from mandos.search.chembl.indication_search import IndicationSearch
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Imports from package mandos are not grouped Loading history...
7
8			from .. import get_test_resource
9
10
11			class TestIndicationSearch:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
12			def test_find(self):
			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... introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
13			df, triples = Commands.trials(get_test_resource("inchis.txt"))
			0 ignored issues – show Coding Style Naming introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
14			assert len(df) == 6
15			assert len(triples) == 6
16			assert {t.compound_name.lower() for t in triples} == {"alprazolam"}
17			assert {t.object_id for t in triples} == {
18			"D012559",
19			"D016584",
20			"D003704",
21			"D001008",
22			"D001007",
23			"D003866",
24			}
25			assert {t.object_name.lower() for t in triples} == {
26			"schizophrenia",
27			"panic disorder",
28			"dementia",
29			"anxiety",
30			"depressive disorder",
31			"anxiety disorders",
32			}
33			assert {t.predicate for t in triples} == {"phase-4 indication", "phase-3 indication"}
34
35			def test_cocaine_hcl(self):
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
36			api = ChemblApi.wrap(Chembl)
37			df, triples = Searcher(IndicationSearch(api, min_phase=3)).search_for(["CHEMBL529437"])
			0 ignored issues – show Coding Style Naming introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
38			assert len(df) == 1
39			assert len(triples) == 1
40			assert triples[0].compound_name.lower() == "cocaine"
41			assert triples[0].compound_id == "CHEMBL370805"
42			assert triples[0].object_id == "D000758"
43			assert triples[0].object_name == "Anesthesia"
44			assert triples[0].predicate == "phase-4 indication"
45
46
47			if __name__ == "__main__":
48			pytest.main()
49

dmyersturnbull / mandos

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TestIndicationSearch.test_find() A

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