From b15531ccd7b8f3eb1cee820b79017109c2536c08 Mon Sep 17 00:00:00 2001
From: Christian Atallah <chrisata@ebi.ac.uk>
Date: Thu, 9 Jan 2025 16:43:19 +0000
Subject: [PATCH] set defaults of Optional taxon fields to None otherwise it
 doesn't work without Pandera

---
 mgnify_pipelines_toolkit/schemas/schemas.py | 34 ++++++++++-----------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/mgnify_pipelines_toolkit/schemas/schemas.py b/mgnify_pipelines_toolkit/schemas/schemas.py
index 99d03d4..4e61a81 100644
--- a/mgnify_pipelines_toolkit/schemas/schemas.py
+++ b/mgnify_pipelines_toolkit/schemas/schemas.py
@@ -158,28 +158,28 @@ class Taxon(BaseModel):
     All of the ranks are optional, to model for the taxon being "Unclassified".
     """
 
-    Superkingdom: Optional[TaxRank]
-    Kingdom: Optional[TaxRank]
-    Phylum: Optional[TaxRank]
-    Class: Optional[TaxRank]
-    Order: Optional[TaxRank]
-    Family: Optional[TaxRank]
-    Genus: Optional[TaxRank]
-    Species: Optional[TaxRank]
+    Superkingdom: Optional[TaxRank] = None
+    Kingdom: Optional[TaxRank] = None
+    Phylum: Optional[TaxRank] = None
+    Class: Optional[TaxRank] = None
+    Order: Optional[TaxRank] = None
+    Family: Optional[TaxRank] = None
+    Genus: Optional[TaxRank] = None
+    Species: Optional[TaxRank] = None
 
 
 class PR2Taxon(BaseModel):
     """Class for modelling the same thing as the preceding class, but for PR2 ranks."""
 
-    Domain: Optional[TaxRank]
-    Supergroup: Optional[TaxRank]
-    Division: Optional[TaxRank]
-    Subdivision: Optional[TaxRank]
-    Class: Optional[TaxRank]
-    Order: Optional[TaxRank]
-    Family: Optional[TaxRank]
-    Genus: Optional[TaxRank]
-    Species: Optional[TaxRank]
+    Domain: Optional[TaxRank] = None
+    Supergroup: Optional[TaxRank] = None
+    Division: Optional[TaxRank] = None
+    Subdivision: Optional[TaxRank] = None
+    Class: Optional[TaxRank] = None
+    Order: Optional[TaxRank] = None
+    Family: Optional[TaxRank] = None
+    Genus: Optional[TaxRank] = None
+    Species: Optional[TaxRank] = None
 
 
 class TaxonRecord(Taxon):