From 45428649e5ac358d552699b33354debb19252e8c Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Tue, 23 Jun 2026 11:46:30 -0400
Subject: [PATCH 1/2] feat!: store allele origin as mapping, not extension

close #232
---
 civicpy/exports/civic_gks_record.py | 7 ++++++-
 civicpy/tests/test_exports.py       | 7 ++++++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/civicpy/exports/civic_gks_record.py b/civicpy/exports/civic_gks_record.py
index b9d0eba..0c3546b 100644
--- a/civicpy/exports/civic_gks_record.py
+++ b/civicpy/exports/civic_gks_record.py
@@ -634,7 +634,12 @@ def get_allele_origin_qualifier(record: Evidence | Assertion) -> MappableConcept
 
         return MappableConcept(
             name=VARIANT_ORIGIN_TO_ALLELE_ORIGIN[variant_origin],
-            extensions=[Extension(name="civic_variant_origin", value=variant_origin)],
+            mappings=[
+                ConceptMapping(
+                    coding=Coding(code="SOMATIC", system="https://civicdb.org"),
+                    relation=Relation.EXACT_MATCH,
+                )
+            ],
         )
 
     @staticmethod
diff --git a/civicpy/tests/test_exports.py b/civicpy/tests/test_exports.py
index 2739d52..404bbc0 100644
--- a/civicpy/tests/test_exports.py
+++ b/civicpy/tests/test_exports.py
@@ -368,7 +368,12 @@ def gks_therapeutic_proposition(gks_mpid33, gks_gid19, gks_tid146, gks_did8):
         "geneContextQualifier": gks_gid19,
         "alleleOriginQualifier": {
             "name": "somatic",
-            "extensions": [{"name": "civic_variant_origin", "value": "SOMATIC"}],
+            "mappings": [
+                {
+                    "coding": {"code": "SOMATIC", "system": "https://civicdb.org"},
+                    "relation": "exactMatch",
+                }
+            ],
         },
         "predicate": "predictsSensitivityTo",
         "objectTherapeutic": gks_tid146,

From 6b48250cbd45447b01368d36a0b177a6751ed54b Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Thu, 25 Jun 2026 08:17:59 -0400
Subject: [PATCH 2/2] dont hardcode + apply aw suggestions

---
 civicpy/exports/civic_gks_record.py | 10 +++++++++-
 civicpy/tests/test_exports.py       |  8 +++++++-
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/civicpy/exports/civic_gks_record.py b/civicpy/exports/civic_gks_record.py
index 0c3546b..8ab5058 100644
--- a/civicpy/exports/civic_gks_record.py
+++ b/civicpy/exports/civic_gks_record.py
@@ -636,7 +636,15 @@ def get_allele_origin_qualifier(record: Evidence | Assertion) -> MappableConcept
             name=VARIANT_ORIGIN_TO_ALLELE_ORIGIN[variant_origin],
             mappings=[
                 ConceptMapping(
-                    coding=Coding(code="SOMATIC", system="https://civicdb.org"),
+                    coding=Coding(
+                        code=variant_origin,
+                        system="CIViC Knowledgebase",
+                        iris=[
+                            iriReference(
+                                root="https://civic.readthedocs.io/en/latest/model/evidence/origin.html"
+                            )
+                        ],
+                    ),
                     relation=Relation.EXACT_MATCH,
                 )
             ],
diff --git a/civicpy/tests/test_exports.py b/civicpy/tests/test_exports.py
index 404bbc0..9f0a38c 100644
--- a/civicpy/tests/test_exports.py
+++ b/civicpy/tests/test_exports.py
@@ -370,7 +370,13 @@ def gks_therapeutic_proposition(gks_mpid33, gks_gid19, gks_tid146, gks_did8):
             "name": "somatic",
             "mappings": [
                 {
-                    "coding": {"code": "SOMATIC", "system": "https://civicdb.org"},
+                    "coding": {
+                        "code": "SOMATIC",
+                        "system": "CIViC Knowledgebase",
+                        "iris": [
+                            "https://civic.readthedocs.io/en/latest/model/evidence/origin.html"
+                        ],
+                    },
                     "relation": "exactMatch",
                 }
             ],