diff options
| -rw-r--r-- | gn3/computations/slink.py | 2 | ||||
| -rw-r--r-- | gn3/db/traits.py | 6 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 3 |
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"}], |