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authorMuriithi Frederick Muriuki2021-08-04 11:30:44 +0300
committerMuriithi Frederick Muriuki2021-08-04 11:30:44 +0300
commitf712da630c1a3642cb44b62c4b2b857373cd78d7 (patch)
tree55417c63e2955522769f302c269411b7a2cd5afa
parent0d7ebb87e2995207f23bc8b8e05e64aaab50b48d (diff)
downloadgenenetwork3-f712da630c1a3642cb44b62c4b2b857373cd78d7.tar.gz
Fix issues caught by pylint
* gn3/computations/slink.py: remove unused imports * gn3/db/traits.py: remove unnecessary `else` clauses * tests/unit/db/test_traits.py: add docstrings for functions
-rw-r--r--gn3/computations/slink.py2
-rw-r--r--gn3/db/traits.py6
-rw-r--r--tests/unit/db/test_traits.py3
3 files changed, 7 insertions, 4 deletions
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py
index 23d3d88..5953e6b 100644
--- a/gn3/computations/slink.py
+++ b/gn3/computations/slink.py
@@ -7,7 +7,7 @@ slink:
TODO: Describe what the function does...
"""
import logging
-from typing import List, Tuple, Union, Sequence
+from typing import Union, Sequence
NumType = Union[int, float]
SeqOfNums = Sequence[NumType]
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index ea35d7e..29c91a6 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -166,8 +166,7 @@ def set_confidential_field(trait_info):
"confidential": 1 if (
trait_info.get("pre_publication_description", None)
and not trait_info.get("pubmed_id", None)) else 0}
- else:
- return trait_info
+ return trait_info
def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"""Retrieve trait information for type `ProbeSet` traits.
@@ -344,13 +343,14 @@ def set_riset_fields(trait_info, conn):
def retrieve_trait_info(
trait_type: str, trait_name: str, trait_dataset_id: int,
- trait_dataset_name: str, conn: Any, QTL=None):
+ trait_dataset_name: str, conn: Any, qtl=None):
"""Retrieves the trait information.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
This function, or the dependent functions, might be incomplete as they are
currently."""
+ # pylint: disable=[R0913]
trait_info_function_table = {
"Publish": retrieve_publish_trait_info,
"ProbeSet": retrieve_probeset_trait_info,
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 2445d26..1c481a2 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -207,6 +207,7 @@ class TestTraitsDBFunctions(TestCase):
)
def test_set_haveinfo_field(self):
+ """Test that the `haveinfo` field is set up correctly"""
for trait_info, expected in [
[{}, {"haveinfo": 0}],
[{"k1": "v1"}, {"k1": "v1", "haveinfo": 1}]]:
@@ -214,6 +215,7 @@ class TestTraitsDBFunctions(TestCase):
self.assertEqual(set_haveinfo_field(trait_info), expected)
def test_set_homologene_id_field(self):
+ """Test that the `homologene_id` field is set up correctly"""
for trait_info, expected in [
[{"type": "Publish"},
{"type": "Publish", "homologeneid": None}],
@@ -229,6 +231,7 @@ class TestTraitsDBFunctions(TestCase):
set_homologene_id_field(trait_info, db_mock), expected)
def test_set_confidential_field(self):
+ """Test that the `confidential` field is set up correctly"""
for trait_info, expected in [
[{"type": "Publish"}, {"type": "Publish", "confidential": 0}],
[{"type": "ProbeSet"}, {"type": "ProbeSet"}],