fix(db): add a migration script to correct the many-to-many relations…

…hip between `Study` and `Group`

alembic/versions/fd73601a9075_add_delete_cascade_studies.py

@@ -5,11 +5,12 @@
 Revises: 3c70366b10ea
 Create Date: 2024-02-12 17:27:37.314443
 """
+import sqlalchemy as sa  # type: ignore
 from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "fd73601a9075"
-down_revision = "3c70366b10ea"
+down_revision = "dae93f1d9110"
 branch_labels = None
 depends_on = None
 
@@ -25,6 +26,8 @@
 
 def upgrade() -> None:
     dialect_name: str = op.get_context().dialect.name
+
+    # SQLite doesn't support dropping foreign keys, so we need to ignore it here
     if dialect_name == "postgresql":
         with op.batch_alter_table("rawstudy", schema=None) as batch_op:
             batch_op.drop_constraint(RAWSTUDY_FK, type_="foreignkey")
@@ -38,16 +41,25 @@ def upgrade() -> None:
             batch_op.drop_constraint(VARIANTSTUDY_FK, type_="foreignkey")
             batch_op.create_foreign_key(VARIANTSTUDY_FK, "study", ["id"], ["id"], ondelete="CASCADE")
 
-    elif dialect_name == "sqlite":
-        # Adding ondelete="CASCADE" to a foreign key in sqlite is not supported
-        pass
-
-    else:
-        raise NotImplementedError(f"{dialect_name=} not implemented")
+    with op.batch_alter_table("group_metadata", schema=None) as batch_op:
+        batch_op.alter_column("group_id", existing_type=sa.VARCHAR(length=36), nullable=False)
+        batch_op.alter_column("study_id", existing_type=sa.VARCHAR(length=36), nullable=False)
+        batch_op.create_index(batch_op.f("ix_group_metadata_group_id"), ["group_id"], unique=False)
+        batch_op.create_index(batch_op.f("ix_group_metadata_study_id"), ["study_id"], unique=False)
+        if dialect_name == "postgresql":
+            batch_op.drop_constraint("group_metadata_group_id_fkey", type_="foreignkey")
+            batch_op.drop_constraint("group_metadata_study_id_fkey", type_="foreignkey")
+            batch_op.create_foreign_key(
+                "group_metadata_group_id_fkey", "groups", ["group_id"], ["id"], ondelete="CASCADE"
+            )
+            batch_op.create_foreign_key(
+                "group_metadata_study_id_fkey", "study", ["study_id"], ["id"], ondelete="CASCADE"
+            )
 
 
 def downgrade() -> None:
     dialect_name: str = op.get_context().dialect.name
+    # SQLite doesn't support dropping foreign keys, so we need to ignore it here
     if dialect_name == "postgresql":
         with op.batch_alter_table("rawstudy", schema=None) as batch_op:
             batch_op.drop_constraint(RAWSTUDY_FK, type_="foreignkey")
@@ -61,9 +73,14 @@ def downgrade() -> None:
             batch_op.drop_constraint(VARIANTSTUDY_FK, type_="foreignkey")
             batch_op.create_foreign_key(VARIANTSTUDY_FK, "study", ["id"], ["id"])
 
-    elif dialect_name == "sqlite":
-        # Removing ondelete="CASCADE" to a foreign key in sqlite is not supported
-        pass
-
-    else:
-        raise NotImplementedError(f"{dialect_name=} not implemented")
+    with op.batch_alter_table("group_metadata", schema=None) as batch_op:
+        # SQLite doesn't support dropping foreign keys, so we need to ignore it here
+        if dialect_name == "postgresql":
+            batch_op.drop_constraint("group_metadata_study_id_fkey", type_="foreignkey")
+            batch_op.drop_constraint("group_metadata_group_id_fkey", type_="foreignkey")
+            batch_op.create_foreign_key("group_metadata_study_id_fkey", "study", ["study_id"], ["id"])
+            batch_op.create_foreign_key("group_metadata_group_id_fkey", "groups", ["group_id"], ["id"])
+        batch_op.drop_index(batch_op.f("ix_group_metadata_study_id"))
+        batch_op.drop_index(batch_op.f("ix_group_metadata_group_id"))
+        batch_op.alter_column("study_id", existing_type=sa.VARCHAR(length=36), nullable=True)
+        batch_op.alter_column("group_id", existing_type=sa.VARCHAR(length=36), nullable=True)