Add migration for 0.15.3 data model update (#280)

cidc_schemas/__init__.py

@@ -4,4 +4,4 @@
 
 __author__ = """James Lindsay"""
 __email__ = "jlindsay@jimmy.harvard.edu"
-__version__ = "0.15.3"
+__version__ = "0.15.4"

cidc_schemas/migrations.py

@@ -40,6 +40,29 @@ def downgrade(metadata: dict, *args, **kwargs) -> MigrationResult:
         raise NotImplementedError
 
 
+class v0_15_2_to_v0_15_3(migration):
+    """
+    v0.15.2: allowed_cohort_names included "Not reported" as an allowed value.
+    v0.15.3: allowed_cohort_names was updated to use "Not_reported" instead of "Not reported" for this value.
+    """
+
+    @classmethod
+    def upgrade(cls, metadata: dict, *args, **kwargs) -> MigrationResult:
+        for p in metadata.get("participants", []):
+            if p["cohort_name"] == "Not reported":
+                p["cohort_name"] = "Not_reported"
+
+        return MigrationResult(metadata, {})
+
+    @classmethod
+    def downgrade(cls, metadata: dict, *args, **kwargs):
+        for p in metadata.get("participants", []):
+            if p["cohort_name"] == "Not_reported":
+                p["cohort_name"] == "Not reported"
+
+        return MigrationResult(metadata, {})
+
+
 class v0_10_2_to_v0_11_0(migration):
     """
     v0.11.0 allowed_cohort_names and allowed_collection_event_names were

tests/test_migrations.py

@@ -5,6 +5,7 @@
     v0_10_0_to_v0_10_2,
     MigrationError,
     v0_10_2_to_v0_11_0,
+    v0_15_2_to_v0_15_3,
 )
 
 
@@ -22,6 +23,20 @@ def test_follow_path():
     assert _follow_path(d, 1) is None
 
 
+def test_v0_15_2_to_v0_15_3():
+    assert v0_15_2_to_v0_15_3.downgrade(
+        v0_15_2_to_v0_15_3.upgrade({"foo": "bar"}).result
+    ).result == {"foo": "bar"}
+
+    ct = {"participants": [{"cohort_name": "Not reported"}, {"cohort_name": "foo"}]}
+
+    upgraded_ct = v0_15_2_to_v0_15_3.upgrade(ct).result
+    assert upgraded_ct["participants"][0]["cohort_name"] == "Not_reported"
+    assert upgraded_ct["participants"][1]["cohort_name"] == "foo"
+
+    assert ct == v0_15_2_to_v0_15_3.downgrade(upgraded_ct).result
+
+
 def test_v0_10_2_to_v0_11_0():
 
     empty_ct = {}