tests.model.test_targets.TestTargets.test_find() - Code Metrics - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

tests.model.test_targets.TestTargets.test_find() A
last analyzed 2021-01-25 23:07 UTC

↳ Parent: tests.model.test_targets

Complexity

Conditions

Size

Total Lines	12
Code Lines	11

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	11
nop	1
dl	0
loc	12
rs	9.85
c	0
b	0
f	0

import pytest


from mandos.chembl_api import ChemblApi, ChemblEntrypoint
from mandos.model.targets import Target, TargetFactory, TargetRelationshipType, TargetType


class TestTargets:

    def test_find(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        dat = dict(
            target_chembl_id="CHEMBL4444",
            pref_name="dopamine transporter",
            target_type="SINGLE_PROTEIN",
        )
        api = ChemblApi.mock({"target": ChemblEntrypoint.mock({"DAT": dat})})
        target = TargetFactory.find("DAT", api)
        assert isinstance(target, Target)
        assert target.type == TargetType.single_protein
        assert target.name == "dopamine transporter"
        assert target.chembl == "CHEMBL4444"

    def test_parents(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        dat = dict(
            target_chembl_id="CHEMBL4444",
            pref_name="dopamine transporter",
            target_type="SINGLE_PROTEIN",
        )
        monoamine = dict(
            target_chembl_id="CHEMBL1111",
            pref_name="monoamine transporter",
            target_type="SINGLE_PROTEIN",
        )
        receptor = dict(
            target_chembl_id="CHEMBL0000", pref_name="receptor", target_type="PROTEIN_COMPLEX"
        )
        relations = [
            dict(relationship="SUBSET OF", related_target_chembl_id="CHEMBL1111"),
            dict(relationship="SUBSET OF", related_target_chembl_id="CHEMBL0000"),
        ]
        get_target = {
            "DAT": dat,
            "CHEMBL4444": dat,
            "CHEMBL1111": monoamine,
            "CHEMBL0000": receptor,
        }

        def filter_targets(kwargs):

            x = kwargs["target_chembl_id"]

            if x == "CHEMBL4444":

                return [dat]
            elif x == "CHEMBL1111":
                return [monoamine]
            elif x == "CHEMBL0000":
                return [receptor]

        def filter_relations(kwargs):

            return relations

        api = ChemblApi.mock(
            {
                "target": ChemblEntrypoint.mock(get_target, filter_targets),
                "target_relation": ChemblEntrypoint.mock({}, filter_relations),
            }
        )
        target = TargetFactory.find("CHEMBL4444", api)
        assert len(target.links({TargetRelationshipType.subset_of})) == 2
        # should sort by CHEMBL ID first, so 0000 will be first
        parent, link_type = target.links({TargetRelationshipType.subset_of})[0]

        assert parent.name == "receptor"
        assert parent.chembl == "CHEMBL0000"
        parent, link_type = target.links({TargetRelationshipType.subset_of})[1]
        assert parent.name == "monoamine transporter"
        assert parent.chembl == "CHEMBL1111"

    def test_traverse_gabaa(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        x = dict(

            target_chembl_id="CHEMBL5112",
            pref_name="GABA receptor alpha-5 subunit",
            target_type="SINGLE PROTEIN",
        )
        x_row1 = dict(
            target_chembl_id="CHEMBL2093872",
            pref_name="GABA-A receptor; anion channel",
            target_type="PROTEIN COMPLEX GROUP",
        )
        x_row1_superset = dict(

            target_chembl_id="CHEMBL1111", pref_name="supergroup", target_type="SELECTIVITY FILTER"
        )
        x_row2 = dict(

            target_chembl_id="CHEMBL2094122",
            pref_name="GABA-A receptor; alpha-5/beta-3/gamma-2",
            target_type="PROTEIN COMPLEX",
        )
        x_row3 = dict(

            target_chembl_id="CHEMBL2109243",
            pref_name="GABA-A receptor; benzodiazepine site",
            target_type="PROTEIN COMPLEX GROUP",
        )
        x_row4 = dict(
            target_chembl_id="CHEMBL2109244",
            pref_name="GABA-A receptor; agonist GABA site",
            target_type="PROTEIN COMPLEX GROUP",
        )
        x_row5 = dict(

            target_chembl_id="CHEMBL3885576",
            pref_name="Gamma-aminobutyric acid receptor subunit alpha-5/beta-2",
            target_type="PROTEIN COMPLEX",
        )
        x_row6 = dict(

            target_chembl_id="CHEMBL3885577",
            pref_name="Gamma-aminobutyric acid receptor subunit alpha-5/beta-3/gamma-3",
            target_type="PROTEIN COMPLEX",
        )
        x_row7 = dict(

            target_chembl_id="CHEMBL4296057",
            pref_name="Gamma-aminobutyric acid receptor subunit alpha-5/beta-3",
            target_type="PROTEIN COMPLEX",
        )
        xrow2_row2 = x_row1

        xrow3_row3 = x_row1

        xrow4_row5 = x_row1

        xrow5_row3 = x_row1

        xrow5_row7 = x_row4

        relations = [

            dict(relationship="SUBSET OF", related_target_chembl_id="CHEMBL1111"),
            dict(relationship="SUBSET OF", related_target_chembl_id="CHEMBL0000"),
        ]
        # TODO



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 Missing module docstring Loading history... introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'pytest' Loading history...
2
3			from mandos.chembl_api import ChemblApi, ChemblEntrypoint
4			from mandos.model.targets import Target, TargetFactory, TargetRelationshipType, TargetType
5
6
7			class TestTargets:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
8			def test_find(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... 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...
9			dat = dict(
10			target_chembl_id="CHEMBL4444",
11			pref_name="dopamine transporter",
12			target_type="SINGLE_PROTEIN",
13			)
14			api = ChemblApi.mock({"target": ChemblEntrypoint.mock({"DAT": dat})})
15			target = TargetFactory.find("DAT", api)
16			assert isinstance(target, Target)
17			assert target.type == TargetType.single_protein
18			assert target.name == "dopamine transporter"
19			assert target.chembl == "CHEMBL4444"
20
21			def test_parents(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... 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...
22			dat = dict(
23			target_chembl_id="CHEMBL4444",
24			pref_name="dopamine transporter",
25			target_type="SINGLE_PROTEIN",
26			)
27			monoamine = dict(
28			target_chembl_id="CHEMBL1111",
29			pref_name="monoamine transporter",
30			target_type="SINGLE_PROTEIN",
31			)
32			receptor = dict(
33			target_chembl_id="CHEMBL0000", pref_name="receptor", target_type="PROTEIN_COMPLEX"
34			)
35			relations = [
36			dict(relationship="SUBSET OF", related_target_chembl_id="CHEMBL1111"),
37			dict(relationship="SUBSET OF", related_target_chembl_id="CHEMBL0000"),
38			]
39			get_target = {
40			"DAT": dat,
41			"CHEMBL4444": dat,
42			"CHEMBL1111": monoamine,
43			"CHEMBL0000": receptor,
44			}
45
46			def filter_targets(kwargs):
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Either all return statements in a function should return an expression, or none of them should. Loading history...
47			x = kwargs["target_chembl_id"]
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable 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...
48			if x == "CHEMBL4444":
			0 ignored issues – show unused-code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unnecessary "elif" after "return" Loading history...
49			return [dat]
50			elif x == "CHEMBL1111":
51			return [monoamine]
52			elif x == "CHEMBL0000":
53			return [receptor]
54
55			def filter_relations(kwargs):
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The argument `kwargs` seems to be unused. Loading history...
56			return relations
57
58			api = ChemblApi.mock(
59			{
60			"target": ChemblEntrypoint.mock(get_target, filter_targets),
61			"target_relation": ChemblEntrypoint.mock({}, filter_relations),
62			}
63			)
64			target = TargetFactory.find("CHEMBL4444", api)
65			assert len(target.links({TargetRelationshipType.subset_of})) == 2
66			# should sort by CHEMBL ID first, so 0000 will be first
67			parent, link_type = target.links({TargetRelationshipType.subset_of})[0]
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `link_type` seems to be unused. Loading history...
68			assert parent.name == "receptor"
69			assert parent.chembl == "CHEMBL0000"
70			parent, link_type = target.links({TargetRelationshipType.subset_of})[1]
71			assert parent.name == "monoamine transporter"
72			assert parent.chembl == "CHEMBL1111"
73
74			def test_traverse_gabaa(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Comprehensibility introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This function exceeds the maximum number of variables (16/15). Loading history... 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...
75			x = dict(
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable 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... Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `x` seems to be unused. Loading history...
76			target_chembl_id="CHEMBL5112",
77			pref_name="GABA receptor alpha-5 subunit",
78			target_type="SINGLE PROTEIN",
79			)
80			x_row1 = dict(
81			target_chembl_id="CHEMBL2093872",
82			pref_name="GABA-A receptor; anion channel",
83			target_type="PROTEIN COMPLEX GROUP",
84			)
85			x_row1_superset = dict(
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `x_row1_superset` seems to be unused. Loading history...
86			target_chembl_id="CHEMBL1111", pref_name="supergroup", target_type="SELECTIVITY FILTER"
87			)
88			x_row2 = dict(
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `x_row2` seems to be unused. Loading history...
89			target_chembl_id="CHEMBL2094122",
90			pref_name="GABA-A receptor; alpha-5/beta-3/gamma-2",
91			target_type="PROTEIN COMPLEX",
92			)
93			x_row3 = dict(
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `x_row3` seems to be unused. Loading history...
94			target_chembl_id="CHEMBL2109243",
95			pref_name="GABA-A receptor; benzodiazepine site",
96			target_type="PROTEIN COMPLEX GROUP",
97			)
98			x_row4 = dict(
99			target_chembl_id="CHEMBL2109244",
100			pref_name="GABA-A receptor; agonist GABA site",
101			target_type="PROTEIN COMPLEX GROUP",
102			)
103			x_row5 = dict(
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `x_row5` seems to be unused. Loading history...
104			target_chembl_id="CHEMBL3885576",
105			pref_name="Gamma-aminobutyric acid receptor subunit alpha-5/beta-2",
106			target_type="PROTEIN COMPLEX",
107			)
108			x_row6 = dict(
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `x_row6` seems to be unused. Loading history...
109			target_chembl_id="CHEMBL3885577",
110			pref_name="Gamma-aminobutyric acid receptor subunit alpha-5/beta-3/gamma-3",
111			target_type="PROTEIN COMPLEX",
112			)
113			x_row7 = dict(
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `x_row7` seems to be unused. Loading history...
114			target_chembl_id="CHEMBL4296057",
115			pref_name="Gamma-aminobutyric acid receptor subunit alpha-5/beta-3",
116			target_type="PROTEIN COMPLEX",
117			)
118			xrow2_row2 = x_row1
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `xrow2_row2` seems to be unused. Loading history...
119			xrow3_row3 = x_row1
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `xrow3_row3` seems to be unused. Loading history...
120			xrow4_row5 = x_row1
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `xrow4_row5` seems to be unused. Loading history...
121			xrow5_row3 = x_row1
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `xrow5_row3` seems to be unused. Loading history...
122			xrow5_row7 = x_row4
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `xrow5_row7` seems to be unused. Loading history...
123			relations = [
			0 ignored issues – show Unused Code introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report The variable `relations` seems to be unused. Loading history...
124			dict(relationship="SUBSET OF", related_target_chembl_id="CHEMBL1111"),
125			dict(relationship="SUBSET OF", related_target_chembl_id="CHEMBL0000"),
126			]
127			# TODO
			0 ignored issues – show Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report `TODO` and `FIXME` comments should generally be avoided. Loading history...
128
129
130			if __name__ == "__main__":
131			pytest.main()
132

dmyersturnbull / mandos

tests.model.test_targets.TestTargets.test_find() A last analyzed 2021-01-25 23:07 UTC

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tests.model.test_targets.TestTargets.test_find() A
last analyzed 2021-01-25 23:07 UTC