Fixed failing tests

Author: khoroshevskyi

bbconf/models/bed_models.py

@@ -110,13 +110,13 @@ class StandardMeta(BaseModel):
     """
 
     species_name: str | None = Field(
-        default=None,
+        default="",
         description="Name of species. e.g. Homo sapiens.",
         alias="organism",
     )
-    species_id: str = ""
-    genotype: str = Field("", description="Genotype of the sample")
-    phenotype: str = Field("", description="Phenotype of the sample")
+    species_id: str | None = ""
+    genotype: str | None = Field("", description="Genotype of the sample")
+    phenotype: str | None = Field("", description="Phenotype of the sample")
     description: str | None = ""
 
     cell_type: str | None = Field(

tests/conftest.py

@@ -105,7 +105,7 @@ def example_dict():
             "promoterprox_frequency": 16,
             "promoterprox_percentage": 17,
         },
-        metadata={"sample_name": "sample_name_1"},
+        metadata={"sample_name": "sample_name_1", "species_name": "species_name", "species_id": "123"},
         plots=plots,
         files=files,
         classification=classification,

tests/test_bedfile.py

@@ -215,7 +215,7 @@ def test_bed_update(self, bbagent_obj):
         with ContextManagerDBTesting(config=bbagent_obj.config, add_data=True):
             bed_file = bbagent_obj.bed.get(BED_TEST_ID, full=True)
             # assert bed_file.annotation.model_dump(exclude_defaults=True) == {}
-            assert bed_file.annotation.cell_line == ""
+            assert bed_file.annotation.cell_line is None
 
             new_metadata = {
                 "cell_line": "K562",