fix: pydantic validation of None in enums

zavolanlab · Jun 1, 2022 · b1b4e54 · b1b4e54
1 parent 7392f65
commit b1b4e54
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Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/htsinfer/get_read_orientation.py b/htsinfer/get_read_orientation.py
@@ -585,6 +585,7 @@ def process_paired(  # pylint: disable=R0912,R0915
         if reads >= self.min_mapped_reads:
             if fraction_most_common_state > self.min_fraction:
                 orientation.relationship = most_common_state
+                assert orientation.relationship is not None
                 if orientation.relationship.value[-2:] == "SF":
                     orientation.file_1 = StatesOrientation("SF")
                     orientation.file_2 = StatesOrientation("SR")

diff --git a/htsinfer/models.py b/htsinfer/models.py
@@ -182,9 +182,9 @@ class ResultsType(BaseModel):
         file_2: Library type of the second file.
         relationship: Type/mate relationship between the provided files.
     """
-    file_1: StatesType = StatesType.not_available
-    file_2: StatesType = StatesType.not_available
-    relationship: StatesTypeRelationship = (
+    file_1: Optional[StatesType] = StatesType.not_available
+    file_2: Optional[StatesType] = StatesType.not_available
+    relationship: Optional[StatesTypeRelationship] = (
         StatesTypeRelationship.not_available
     )
 
@@ -270,9 +270,9 @@ class ResultsOrientation(BaseModel):
         file_1: Read orientation of first file.
         file_2: Read orientation of second file.
     """
-    file_1: StatesOrientation = StatesOrientation.not_available
-    file_2: StatesOrientation = StatesOrientation.not_available
-    relationship: StatesOrientationRelationship = (
+    file_1: Optional[StatesOrientation] = StatesOrientation.not_available
+    file_2: Optional[StatesOrientation] = StatesOrientation.not_available
+    relationship: Optional[StatesOrientationRelationship] = (
         StatesOrientationRelationship.not_available
     )